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:

http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?revision=1.416&root=ensembl&view=markup

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”

When there are multiple annotation extensions separated by commas, need to split them and populate each relation(entity) separately.

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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