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 in this directory on mangolassi:
/home/postgres/work/pgpopulation/go/go_curation/20141106_kevin_godata/newGpaEntries
3. Mapping of columns in the newGpaEntries file to GO OA tables is here:
http://wiki.wormbase.org/index.php/Mapping_the_GAF_to_GO_OA_tables
4. Once file is read into OA tables, then we’ll need a new dumping script.
Specs for new OA dumping script
Model for WS248:
1. 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”
2. Gene
From gop_wbgene
Gene “WBGene00004362”
3. GO_code
From gop_goinference
GO_code “IMP”
4. 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”
5. 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_variation
Variation “WBVar00278468”
gop_with_RNAi
RNAi_result “WBRNAi00035226”
gop_with_phenotype
Phenotype “WBPhenotype:0000059”
6. Annotation_extension
Same syntax, relation(entity) e.g., has_regulation_target(WB:WBGene00002015) Tag used depends on what type of entity is in parenthesis
go_xrefto
If entity = WBls:nnnnnn Life_stage_relation “relation” “WBlsnnnnn”
If entity = WB:WBGenennnnnnnn Gene_relation “relation” “WBGenennnnnnnn”
If entity = ChEBI:nnnnn Map ChEBI:nnnnn to WBMol Molecule_relation “relation” “WBMolnnnnnnn”
If entity = WB:WBbtnnnnnnn Anatomy_relation “relation” “WBbtnnnnnnn”
If entity = GO:GOnnnnnnn GO_term_relation “relation” “GO:nnnnnnn”
7. gop_protein (don’t have any at the moment)
Annotation_isoform “UniProtKB:nnnnnn”
9. gop_paper
Reference “WBPaper00028482”
10. gop_accession
GO_reference “Gene Ontology Consortium” “GO_REF” “nnnnnnn”
11. Contributed_by “WormBase”
This will be a default value.
12. gop_lastupdate
Date_last_updated “YYYY-MM-DD”
