Merge pull request #96 from occ-data/master

Master

Author: cgmeyer

…y/schemas/quantification_assay_peak.yaml …sed_nodes/quantification_assay_peak.yamlgdcdictionary/schemas/quantification_assay_peak.yaml renamed to gdcdictionary/old_unused_nodes/quantification_assay_peak.yaml gdcdictionary/schemas/quantification_assay_peak.yaml renamed to gdcdictionary/old_unused_nodes/quantification_assay_peak.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "quantification_assay_peak"
 title: Quantification Assay Peak
 type: object
-namespace: https://www.bloodpac.org
+namespace: https://data.bloodpac.org
 category: notation
 program: '*'
 project: '*'

…ary/schemas/quantification_assay_qc.yaml …nused_nodes/quantification_assay_qc.yamlgdcdictionary/schemas/quantification_assay_qc.yaml renamed to gdcdictionary/old_unused_nodes/quantification_assay_qc.yaml gdcdictionary/schemas/quantification_assay_qc.yaml renamed to gdcdictionary/old_unused_nodes/quantification_assay_qc.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "quantification_assay_qc"
 title: Quantification Assay QC
 type: object
-namespace: https://www.bloodpac.org
+namespace: https://data.bloodpac.org
 category: data_file
 program: '*'
 project: '*'

gdcdictionary/schemas/_definitions.yaml

@@ -206,6 +206,8 @@ data_file_properties:
     $ref: "#/data_file_error_type"
   object_id:
     $ref: "#/object_id"
+  state:
+    $ref: "#/state"
 
 workflow_properties:
   $ref: "#/ubiquitous_properties"

gdcdictionary/schemas/_terms.yaml

@@ -283,6 +283,30 @@ ann_arbor_tumor_stage:
     cde_version: null
     term_url: null
 
+assay_instrument:
+  description: "The specific instrument type used to perform the assay. If applicable, please also indicate the instrument mode and model in 'assay_instrument_mode' and 'assay_instrument_model'."
+
+assay_instrument_mode:
+  description: "The specific mode an instrument was run in (e.g., High Sensitivity). Please, also indicate the instrument and model in 'assay_instrument' and 'assay_instrument_model'."
+
+assay_instrument_model:
+  description: "The specific model of instrument used to perform the assay. Please also indicate the instrument and mode in 'assay_instrument' and 'assay_instrument_mode'."
+
+assay_kit_name:
+  description: "The name of the kit used for the test or assay; please also indicate the kit vendor and version in 'assay_kit_vendor' and 'assay_kit_version'."
+
+assay_kit_vendor:
+  description: "The name of the vendor or manufacturer of the kit used for the test; please also indicate the kit name and version in 'assay_kit_name' and 'assay_kit_version'."
+
+assay_kit_version:
+  description: "The version of the kit used for the test; please also indicate the kit name and vendor in 'assay_kit_name' and 'assay_kit_vendor'."
+
+assay_method:
+  description: "General methodology used to perform the assay."
+
+assay_target:
+  description: "Target for the assay: can be a specific gene, protein, or otherwise."
+
 base_caller_name: # TOREVIEW
   description: >
     Name of the base caller.
@@ -638,6 +662,12 @@ encoding:
     cde_version: null
     term_url: "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/1%20Basic%20Statistics.html"
 
+equipment_manufacturer:
+  description: "The name of the manufacturer of the equipment used for the test; please also indicate the model number in 'equipment_model'."
+
+equipment_model:
+  description: "The equipment name and model number used for the test; please also indicate the manufacturer name in 'equipment_manufacturer'."
+
 estrogen_receptor_percent_positive_ihc:
   description: >
     Classification to represent ER Positive results expressed as a percentage value.

gdcdictionary/schemas/acknowledgement.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "acknowledgement"
 title: Acknowledgement
 type: object
-namespace: https://www.bloodpac.org
+namespace: https://data.bloodpac.org
 category: administrative
 program: '*'
 project: '*'
@@ -37,33 +37,11 @@ required:
   - projects
 
 properties:
-  type:
-    enum: [ "acknowledgement" ]
-
-  id:
-    $ref: "_definitions.yaml#/UUID"
-    systemAlias: node_id
-
-  state:
-    $ref: "_definitions.yaml#/state"
-
-  submitter_id:
-    type:
-      - string
-      - "null"
+  $ref: "_definitions.yaml#/ubiquitous_properties"
 
   acknowledgee:
     description: "The individual or group being acknowledged by the project."
     type: string
 
   projects:
     $ref: "_definitions.yaml#/to_many_project"
-
-  project_id:
-    type: string
-
-  created_datetime:
-    $ref: "_definitions.yaml#/datetime"
-
-  updated_datetime:
-    $ref: "_definitions.yaml#/datetime"

gdcdictionary/schemas/aligned_reads_index.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "aligned_reads_index"
 title: Aligned Reads Index
 type: object
-namespace: https://www.bloodpac.org
+namespace: https://data.bloodpac.org
 category: index_file
 program: '*'
 project: '*'

gdcdictionary/schemas/alignment_workflow.yaml

@@ -3,7 +3,7 @@ $schema: "http://json-schema.org/draft-04/schema#"
 id: "alignment_workflow"
 title: Alignment Workflow
 type: object
-namespace: https://www.bloodpac.org
+namespace: https://data.bloodpac.org
 category: analysis
 program: '*'
 project: '*'

gdcdictionary/schemas/aliquot.yaml

@@ -4,7 +4,7 @@ id: "aliquot"
 title: Aliquot
 type: object
 category: biospecimen
-namespace: https://www.bloodpac.org
+namespace: https://data.bloodpac.org
 program: '*'
 project: '*'
 description: >
@@ -37,12 +37,21 @@ uniqueKeys:
   - [project_id, submitter_id]
 
 links:
-  - name: samples
-    backref: aliquots
-    label: derived_from
-    multiplicity: many_to_many
-    target_type: sample
+  - exclusive: false
     required: true
+    subgroup:
+      - name: samples
+        backref: analytes
+        label: derived_from
+        multiplicity: many_to_many
+        target_type: sample
+        required: false
+      - name: studies
+        backref: analytes
+        label: analyzed_for
+        target_type: study
+        multiplicity: many_to_many
+        required: false
 
 constraints: null
 
@@ -55,53 +64,65 @@ properties:
       - Serum Card
       - Slide
       - Vial
+
   aliquot_quantity:
     description: "The quantity in micrograms (ug) of the aliquot derived from the sample and used for experimentation."
     type: number
+
   aliquot_volume:
     description: "The volume in microliters (uL) of the aliquot derived from the sample and used for experimentation."
     type: number
+
   clinical_or_contrived:
     description: "Is the aliquot clinical or contrived?"
     enum:
       - Clinical
       - Contrived
+
   contrivance_method:
     description: >
       The name or general description of the contrivance(s) added to the biological aliquot.
       Alternatively, if you have provided a contrivance protocol, enter its file_name here.
     type: string
+
   hours_to_freezer_lower:
     description: >
       The lower limit on the amount of time, in hours, that it took between the sample being
       fractionated and the aliquot being frozen or otherwise preserved. If the exact time is known,
-      make this value equal to that of the upper limit. If the time is completely unknown, enter
-      Unknown. If no fractionation was performed on this sample, enter Not Applicable.
-    type:
-      - number
-      - string
-    oneOf:
-      - enum:
-          - Not Applicable
-          - Unknown
-      - type: number
+      make this value equal to that of the upper limit. If the time is completely unknown or if no
+      fractionation was performed on this sample, enter the appropriate value in hours_to_freezer_lower_other.
+    type: number
+
   hours_to_freezer_upper:
     description: >
       The upper limit on the amount of time, in hours, that it took between the sample being
       fractionated and the aliquot being frozen or otherwise preserved. If the exact time is known,
-      make this value equal to that of the lower limit. If the time is completely unknown, enter
-      Unknown. If no fractionation was performed on this sample, enter Not Applicable.
-    type:
-      - number
-      - string
-    oneOf:
-      - enum:
-          - Not Applicable
-          - Unknown
-      - type: number
+      make this value equal to that of the lower limit. If the time is completely unknown or if no
+      fractionation was performed on this sample, enter the appropriate value in hours_to_freezer_upper_other.
+    type: number
+
+  hours_to_freezer_lower_other:
+    description: >
+      If the lower limit on the amount of time, in hours, that it took between the sample being
+      fractionated and the aliquot being frozen or otherwise preserved is completely unknown or
+      if no fractionation was performed on this sample, enter the appropriate value here.
+    enum:
+      - Not Applicable
+      - Unknown
+
+  hours_to_freezer_upper_other:
+    description: >
+      If the upper limit on the amount of time, in hours, that it took between the sample being
+      fractionated and the aliquot being frozen or otherwise preserved is completely unknown or
+      if no fractionation was performed on this sample, enter the appropriate value here.
+    enum:
+      - Not Applicable
+      - Unknown
+
   methanol_added:
     description: "In the preparation of a slide, was methanol added as a fixative? True/False."
     type: boolean
+
   preservation_method:
     term:
       $ref: "_terms.yaml#/preservation_method"
@@ -113,9 +134,13 @@ properties:
       - Snap Frozen
       - Frozen
       - Unknown
+
   storage_temperature:
     description: "The temperature, in centrigrade, at which the aliquot was preserved and/or stored."
     type: number
 
   samples:
-    $ref: "_definitions.yaml#/to_one"
+    $ref: "_definitions.yaml#/to_many"
+
+  studies:
+    $ref: "_definitions.yaml#/to_many"