Noctua - Upload of WB Manual Annotations

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GOC GPAD/GPI 2.0 Specifications

OA Annotations

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='. If no ORICD, add 'GOC:cab1' contributor-id= 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
has_direct_input GOREL:0000752
in_absence_of GOREL:0000755
in_presence_of GOREL:0000027
localization_dependent_on GOREL:0000009
RO:0002211_activity_of GOREL:0098702

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


  • What about blank OA entries, e.g. pgid 14222?
    • Blank entries were ignored.

Protein2GO Annotations

GPAD 2.0 column number GPAD 2.0 column name Action Example
1 Annotated entity Convert each UniProtKB: accession to a WB:WBGene id using the latest WB gpi file WB:WBGene00006925
2 Negation Leave as is NOT
3 Qualifier Leave as is RO:0001025
4 GO term ID Leave as is GO:0051306
5 Reference Leave PMID or DOI as is; add corresponding WB:WBPaper id; identifiers are pipe-separated PMID:10978280|WB:WBPaper00004310
6 Evidence Leave as is ECO:0000314
7 With/From Check UniProtKB: entries for possible conversion to WB:WBGene; otherwise leave entry as is WB:WBGene00000001
8 Interacting taxon Leave as is NCBITaxon:273526
9 Annotation date Leave as is 2006-02-03T12:26
10 Assigned_by Leave as it WB
11 Annotation extensions If relation is a text string, convert to an id according RO mapping table. Otherwise, leave as is. RO:0002233(WB:WBGene00000584)
12 Annotation properties* Most will stay as is, except for history (see below). contributor-id= by Kimberly Van Auken|model-state=deleted

*Annotation Properties

  • Contributor
    • Most contributors are captured with an orcid.
    • However, Carol and Josh do not have orcids, so we need to populate a GOC abberviation for their contributor id.
      • If contributor-id is blank, and comment=action:Added by Josh Jaffery [Expired account], then populate contributor-id=GOC:jja
      • If contributor-id is blank, and comment=action:Added by Carol Bastiani [Expired account], then populate contributor-id=GOC:cab1
  • Examine annotation id; if more than one line with same id, check corresponding date field; for most recent date, leave as is and keep in file for further processing; for earlier dates, add model-state=deleted to annotation properties field (12) and move to separate file that will not be further processed

Final File for Import

  • The final file for import will be a concatenated file of OA, Protein2GO current, and Protein2GO history files.
  • We'll need to make the available for Dustin to import.