GOC GPAD/GPI 2.0 Specifications
https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md
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=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
|
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
|
Questions
- What about blank OA entries, e.g. pgid 14222?
- Blank entries were ignored.
Protein2GO Annotations
- Input files:
- Other mappings needed:
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 |
Examine annotation id; if more than one line with same id, check date field, for most recent date, leave as is; for earlier dates, add model-state=deleted |
id=WBOA:3565
|