Populating the OA and New Dumping Script
1. Need to populate postgres (GO OA tables with data from Phenotype2GO file)
2. File to parse into postgres is currently in this directory on mangolassi:
/home/postgres/work/pgpopulation/go/go_curation/20141106_kevin_godata/newGpaEntries
3. Table mapping columns in the newGpaEntries file to GO OA tables is here:
http://wiki.wormbase.org/index.php/Mapping_the_GAF_to_GO_OA_tables
Will need to add three values to the Qualifier drop-down menu, ‘enables’, ‘involved_in’, ‘part_of’
4. Once file is read into OA tables, then we’ll need a new dumping script.
5. Specs for new OA dumping script
Model for WS248:
Can likely borrow a lot from the gpad parsing script on tazendra /home/acedb/kimberly/citace_upload/go/go_gpad_parser.pl
- Annotation ID
Will need to determine what the starting ID should be Could look at the main .ace file (from gpad conversion - gp_annotation.ace) and start with +1 from the end Currently, that file is on tazendra here: /home/acedb/kimberly/citace_upload/go/gp_annotation.ace
GO_annotation : “00055495”
- Gene
From gop_wbgene
Gene “WBGene00004362”
- GO_term
From gop_goid
GO_term "GO:0005634"
- GO_code
From gop_goinference
GO_code “IMP”
- Annotation_relation
From gop_qualifier Will need to add three values to the drop-down menu, ‘enables’, ‘involved_in’, ‘part_of’ Then populate all ‘P’ with ‘involved_in’; all ‘F’ with ‘enables’, all ‘C’ with ‘part_of’ Can be a multi-value field, i.e., can have something like ‘NOT’ ‘enables’
Annotation_relation “enables”
Annotation_relation “NOT”
Annotation_relation “enables”
- Annotation_made_with
gop_with_wbgene
Interacting_gene “WBGene00000936”
Multiple entries
Interacting_gene “WBGene00000936” Interacting_gene “WBGene00000937”
gop_with
Inferred_from_GO_term “GO:0035195"
gop_with_wbvariation
Variation “WBVar00278468”
gop_with_RNAi
RNAi_result “WBRNAi00035226”
gop_with_phenotype
Phenotype “WBPhenotype:0000059”
- Annotation_extension
gop_xrefto
Syntax: relation(entity)
e.g., has_regulation_target(WB:WBGene00002015)
e.g., happens_during(WBls:00234)
Tag used depends on what type of entity is in parenthesis
If entity = WBls:nnnnnn
Life_stage_relation “relation” “WBls:nnnnn”
If entity = WB:WBGenennnnnnnn Gene_relation “relation” “WBGenennnnnnnn”
If entity = WBMol:nnnnnnn Molecule_relation “relation” “WBMol:nnnnnnn”
If entity = WBbt:nnnnnnn Anatomy_relation “relation” “WBbt:nnnnnnn”
If entity = GO:nnnnnnn GO_term_relation “relation” “GO:nnnnnnn”
Note:When there are multiple annotation extensions separated by commas, need to split them and populate each relation(entity) separately. On mangolassi see pgid 14233 in the GO OA for an example.
Example:
has_regulation_target(WB:WBGene00002015),happens_during(GO:0001666)
Gene_relation "has_regulation_target" "WBGene00002015"
GO_term_relation "happens_during" "GO:0001666"
- gop_protein (don’t have any at the moment)
Annotation_isoform “UniProtKB:nnnnnn”
- gop_paper
Reference “WBPaper00028482”
- gop_accession
GO_reference “Gene Ontology Consortium” “GO_REF” “nnnnnnn”
- Contributed_by “WormBase”
This will be a default value.
- gop_lastupdate
Date_last_updated “YYYY-MM-DD”
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