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Process term curation and Process curation
kyook edited this page Sep 6, 2012
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6 revisions
Fields are OA field name -- postgres table name -- .ace Tag --
TAB1
- Curator -- prt_curator -- dropdown
- WBbioprID -- prt_processid -- WBProcess -- (this field is required by the OA) auto-incremental based on new record dump as WBProcess:"WBbiopr:00000000" 8 digits
- Process name -- prt_processname -- Public_name -- .ace dump as Public_name -- text
- Summary -- prt_summary -- Summary -- big text
- Other_name -- prt_othername -- Other_name -- big text, values will be pipe separated (note that looking for a process term in an OA WBProcess field will autocomplete first on WBbioprID, then process name, then this field. If you don't want this field to trigger autocomplete, let me know)
- Related_process -- prt_relprocess -- Related_process -- XREF to WBProcess -multi-ontology field, autocomplete on Process Term OA objects.
- Remark -- prt_remark -- Remark -- big text
- Paper -- prt_paper -- Reference -- multi-ontology autocomplete on WBPaperID
package is get_process_ace.pm
script is use_process_package.pl
the following must be true:
- Unique WBProcessID
- Unique Process name
- Curator not blank
- Process summary not blank
Fields are OA field name -- postgres table name -- .ace Tag --
TAB1
- Curator -- pro_curator -- dropdown
- Paper -- pro_paper -- Paper_evidence -- single ontology, autocomplete on WBPaperID; term info-WBProcess, Gene, GO terms (need to clear this w/ everyone)
- Process -- pro_process -- WBProcess -- single ontology (required field by OA) autocomplete (term and syn), store WBProcessID, term info, WBProcess ID, WBProcess, Summary, other_name, WBPaper
- GO_term -- pro_goid -- GO_term --pro_paper #evidence-- multi-ontology autocomplete (name and syn); term info -description
- Gene -- pro_wbgene -- pro_paper #evidence-- Gene -- multi-ontology, autocomplete (public_name); term info-name, WBGeneID, WBProcess, WBPaper
- Phenotype -- pro_phenotype -- Phenotype --pro_paper #evidence-- multi-ontology, autocomplete (name and syn); term info -description
- Molecule -- pro_molecule -- Molecule -- pro_paper #evidence -- multi-ontology autocomplete (name and syn);term info-molecule ID, name, syn
- Anatomy_term -- pro_anatomy -- Anatomy_term -- pro_paper #evidence-- multi-ontology autocomplete on name; term info- name, WBbt ID, store ID
- Life_stage -- pro_lifestage -- Life_stage -- pro_paper #evidence-- multi-ontology autocomplete on name; term info- name, store Life_stage ID
- Taxon -- pro_taxon-- NCBITaxonomyID -- multi-ontology of NCBITaxonomy ID, autocomplete on species name
- Expression_cluster -- pro_exprcluster -- Expression_cluster -- pro_paper #evidence-- multi-ontology
- Human_disease -- pro_humdisease -- text -- not in the model-- multi-ontology autocomplete on name and synonym text until file is ready for obo_ table
- Picture -- pro_picture -- Picture -- pro_paper #evidence-- multi-ontology from picture OA table autocomplete on WBPaperID; term info -WBPicture, description, expr. I remember we talked about this field, but not what we said, you'll be doing curation to pictures from here instead of picture curation adding processes ? -- J Yes --K
- Movie -- pro_movie -- Movie -- pro_paper #evidence-- text -- until your file is ready for obo_ table
- Pathway -- pro_pathwaydb -- dump the same way it is dumped for Interaction bigtext -- until file is ready for obo_ table, see http://wiki.wormbase.org/index.php/Gene_Interaction#Instructions_on_How_to_Use_the_New_OA for how to enter data.
package is get_process_curation_ace.pm
script is use_process_curation_package.pl