Difference between revisions of "Noctua - Upload of WB Manual Annotations"

From WormBaseWiki
Jump to navigationJump to search
Line 40: Line 40:
 
| 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. || -
+
| - || 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

Revision as of 19:28, 18 May 2020

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?