Difference between revisions of "Noctua - Upload of WB Manual Annotations"
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*[https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md GPAD/GPI 2.0 specs on github] | *[https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md GPAD/GPI 2.0 specs on github] | ||
+ | |||
+ | = GOC GPAD/GPI 2.0 Specifications = | ||
+ | https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md | ||
= Mapping from gop_ postgres tables to GPAD 2.0 column = | = Mapping from gop_ postgres tables to GPAD 2.0 column = | ||
+ | |||
+ | Skip all entries that have the value 'False Positive' in gop_falsepositive | ||
{| cellspacing="2" border="1" | {| cellspacing="2" border="1" | ||
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| gop_qualifier || 3 || Map text value to Relations Ontology (RO) term id (see below); add RO id. || RO:0001025 | | gop_qualifier || 3 || Map text value to Relations Ontology (RO) term id (see below); add RO id. || RO:0001025 | ||
|- | |- | ||
− | | gop_goid || 4|| Add GO term id. || GO:0051306 | + | | gop_goid || 4|| Add GO term id as it exists in table. || GO:0051306 |
|- | |- | ||
| gop_accession || 5 || Add id as it exists in table. || GO_REF:0000015 | | gop_accession || 5 || Add id as it exists in table. || GO_REF:0000015 | ||
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| gop_with_wbvariation || 7 || Preface each value with 'WB:'; comma-separate multiple values || WB:WBVar00242156 | | gop_with_wbvariation || 7 || Preface each value with 'WB:'; comma-separate multiple values || WB:WBVar00242156 | ||
|- | |- | ||
− | | | + | | - || 8 || No action; I don't think we have any values for an interacting taxon. || |
|- | |- | ||
| gop_lastupdate || 9 || If YYYY-MM-DD, add as exists in table. If YYYY-MM-DD HH:MM:SS convert to: YYYY-MM-DDTHH:MM || 2020-05-13 or 2006-02-03T12:26 | | gop_lastupdate || 9 || If YYYY-MM-DD, add as exists in table. If YYYY-MM-DD HH:MM:SS convert to: YYYY-MM-DDTHH:MM || 2020-05-13 or 2006-02-03T12:26 | ||
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| no OA table || 10 || Add WB || WB | | no OA table || 10 || Add WB || WB | ||
|- | |- | ||
− | | gop_xrefto || 11 || Convert relation name to RO id, add | + | | gop_xrefto || 11 || Convert relation name to RO id, add value, directly and parenthetically, after RO id. || RO:0002233(WB:WBGene00000584) |
|- | |- | ||
| ?? || 12 || Add postgres annotation id, prefixed with 'id=WBOA:' || id=WBOA:3565 | | ?? || 12 || Add postgres annotation id, prefixed with 'id=WBOA:' || id=WBOA:3565 | ||
|- | |- | ||
− | | gop_curator || 12 || If available, map curator to ORCID and prefix with 'contributor-id=https://orcid.org/'. If no ORICD, add 'GOC:cab1' || contributor-id=https://orcid.org/0000-0002-1478-7671 | + | | gop_curator || 12 || If available, map curator to ORCID and prefix with 'contributor-id=https://orcid.org/'. If no ORICD, add 'GOC:cab1' || contributor-id=https://orcid.org/0000-0002-1478-7671 or GOC:cab1 |
|- | |- | ||
| gop_comment || 12 || Add free text, prefixed with 'comment=' || comment=2020-03-17; flagged FP prior to Noctua upload; no ISS With/From; more specific PAINT annotation exists. | | gop_comment || 12 || Add free text, prefixed with 'comment=' || comment=2020-03-17; flagged FP prior to Noctua upload; no ISS With/From; more specific PAINT annotation exists. |
Revision as of 19:28, 18 May 2020
Contents
GOC GPAD/GPI 2.0 Specifications
https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md
Mapping from gop_ postgres tables to GPAD 2.0 column
Skip all entries that have the value 'False Positive' in gop_falsepositive
gop_ postgres table name | GPAD 2.0 column | Action | Example |
---|---|---|---|
gop_wbgene | 1 | Preface each value with 'WB:' | WB:WBGene00006925 |
gop_qualifier | 2 | Add text string "NOT" (Note: an OA query for "NOT" didn't return any values, so I don't think we actually have any of these in the OA.) | NOT |
gop_qualifier | 3 | Map text value to Relations Ontology (RO) term id (see below); add RO id. | RO:0001025 |
gop_goid | 4 | Add GO term id as it exists in table. | GO:0051306 |
gop_accession | 5 | Add id as it exists in table. | GO_REF:0000015 |
gop_paper | 5 | Add WBPaper ID and corresponding PMID, pipe separated. | PMID:10978280|WB:WBPaper00004310 |
gop_goinference | 6 | Map three-letter GO code to ECO code (see below); add ECO id. | ECO:0000314 |
gop_with_wbgene | 7 | Preface each value with 'WB:'; comma-separate multiple values | WB:WBGene00000001 |
gop_with | 7 | Add id as it exists in table; comma-separate multiple values | FB:FBgn0003719 |
gop_with_phenotype | 7 | Add id as it exists in table; comma-separate multiple values | WBPhenotype:0000689 |
gop_with_rnai | 7 | Preface each value with 'WB:'; comma-separate multiple values | WB:WBRNAi00001974 |
gop_with_wbvariation | 7 | Preface each value with 'WB:'; comma-separate multiple values | WB:WBVar00242156 |
- | 8 | No action; I don't think we have any values for an interacting taxon. | |
gop_lastupdate | 9 | If YYYY-MM-DD, add as exists in table. If YYYY-MM-DD HH:MM:SS convert to: YYYY-MM-DDTHH:MM | 2020-05-13 or 2006-02-03T12:26 |
no OA table | 10 | Add WB | WB |
gop_xrefto | 11 | Convert relation name to RO id, add value, directly and parenthetically, after RO id. | RO:0002233(WB:WBGene00000584) |
?? | 12 | Add postgres annotation id, prefixed with 'id=WBOA:' | id=WBOA:3565 |
gop_curator | 12 | If available, map curator to ORCID and prefix with 'contributor-id=https://orcid.org/'. If no ORICD, add 'GOC:cab1' | contributor-id=https://orcid.org/0000-0002-1478-7671 or GOC:cab1 |
gop_comment | 12 | Add free text, prefixed with 'comment=' | comment=2020-03-17; flagged FP prior to Noctua upload; no ISS With/From; more specific PAINT annotation exists. |
Mapping relation names to RO ids.
qualifier name (gop_qualifier) | RO ID |
---|---|
part_of | BFO:0000050 |
enables | RO:0002327 |
acts_upstream_of_or_within | RO:0002264 |
colocalizes_with | RO:0002325 |
involved_in | RO:0002331 |
located_in | RO:0001025 |
contributes_to | RO:0002326 |
has_input | RO:0002233 |
happens_during | RO:0002092 |
Mapping three-letter GO codes to ECO ids.
three-letter GO code | ECO ID |
---|---|
ISS | ECO:0000250 |
IEP | ECO:0000270 |
NAS | ECO:0000303 |
TAS | ECO:0000304 |
IC | ECO:0000305 |
ND | ECO:0000307 |
IDA | ECO:0000314 |
IMP | ECO:0000315 |
IGI | ECO:0000316 |
IPI | ECO:0000353 |
Questions
- What about blank OA entries, e.g. pgid 14222?