Difference between revisions of "Populating the OA and New Dumping Script"
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1. Need to populate postgres (GO OA tables with data from Phenotype2GO file) | 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: | + | 2. File to parse into postgres is currently in this directory on mangolassi: |
/home/postgres/work/pgpopulation/go/go_curation/20141106_kevin_godata/newGpaEntries | /home/postgres/work/pgpopulation/go/go_curation/20141106_kevin_godata/newGpaEntries | ||
| − | 3. | + | 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 | 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’ | |
| − | Specs for new OA dumping script | + | 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: | Model for WS248: | ||
| Line 17: | Line 19: | ||
http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?revision=1.416&root=ensembl&view=markup | http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/wormbase/wspec/models.wrm?revision=1.416&root=ensembl&view=markup | ||
| − | + | *Annotation ID | |
Will need to determine what the starting ID should be | 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 | Could look at the main .ace file (from gpad conversion - gp_annotation.ace) and start with +1 from the end | ||
| Line 25: | Line 27: | ||
| − | + | *Gene | |
From gop_wbgene | From gop_wbgene | ||
| Line 31: | Line 33: | ||
| − | + | *GO_code | |
From gop_goinference | From gop_goinference | ||
| Line 37: | Line 39: | ||
| − | + | *Annotation_relation | |
From gop_qualifier | From gop_qualifier | ||
Will need to add three values to the drop-down menu, ‘enables’, ‘involved_in’, ‘part_of’ | Will need to add three values to the drop-down menu, ‘enables’, ‘involved_in’, ‘part_of’ | ||
| Line 49: | Line 51: | ||
| − | + | *Annotation_made_with | |
gop_with_wbgene | gop_with_wbgene | ||
| Line 66: | Line 68: | ||
| − | + | gop_with_variation | |
Variation “WBVar00278468” | Variation “WBVar00278468” | ||
| Line 81: | Line 83: | ||
| − | + | *Annotation_extension | |
Same syntax, relation(entity) | Same syntax, relation(entity) | ||
| Line 106: | Line 108: | ||
| − | + | *gop_protein (don’t have any at the moment) | |
Annotation_isoform “UniProtKB:nnnnnn” | Annotation_isoform “UniProtKB:nnnnnn” | ||
| − | + | *gop_paper | |
Reference “WBPaper00028482” | Reference “WBPaper00028482” | ||
| − | + | *gop_accession | |
GO_reference “Gene Ontology Consortium” “GO_REF” “nnnnnnn” | GO_reference “Gene Ontology Consortium” “GO_REF” “nnnnnnn” | ||
| − | + | *Contributed_by “WormBase” | |
This will be a default value. | This will be a default value. | ||
| − | + | *gop_lastupdate | |
Date_last_updated “YYYY-MM-DD” | Date_last_updated “YYYY-MM-DD” | ||
Revision as of 17:59, 19 February 2015
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:
- 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_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_variation
Variation “WBVar00278468”
gop_with_RNAi
RNAi_result “WBRNAi00035226”
gop_with_phenotype
Phenotype “WBPhenotype:0000059”
- 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”
- 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”
