Difference between revisions of "Noctua - Upload of WB Manual Annotations"
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− | | 1 || Annotated entity* || Convert each UniProtKB: accession to a | + | | 1 || Annotated entity* || Convert each UniProtKB: accession to a WBGene id using the latest WB gpi file || UniProtKB:G5ED58 || WB:WBGene00006925 || Yes |
|- | |- | ||
| 2|| Negation || Leave as is || NOT || NOT || No | | 2|| Negation || Leave as is || NOT || NOT || No | ||
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| 6 || Evidence || Leave as is || ECO:0000314 || ECO:00000314 || No | | 6 || Evidence || Leave as is || ECO:0000314 || ECO:00000314 || No | ||
|- | |- | ||
− | | 7 || With/From || | + | | 7 || With/From* || Leave as is, except for UniProtKB: accessions; for UniProtKB: accessions, try to map to a WBGene id using the latest WB gpi file; if UniProtKB: accession doesn't map to a WBGene id, then leave as is || UniProtKB:D9PTP8 || WB:WBGene00013354 || Yes - output a list of UniProtKB accessions that didn't map to a WBGene |
|- | |- | ||
| 8 || Interacting taxon || Leave as is || NCBITaxon:273526 | | 8 || Interacting taxon || Leave as is || NCBITaxon:273526 | ||
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=== References === | === References === | ||
* Map incoming doi or PMID to WBPaper id using the pap_identifier table. | * Map incoming doi or PMID to WBPaper id using the pap_identifier table. | ||
+ | |||
+ | === With/From === | ||
+ | * Use latest WormBase gpi file to map UniProtKB accessions (column 1 in incoming GPAD file; column 9 in WB gpi file) to corresponding WBGene ID (column 2 in WB gpi file) | ||
+ | * Latest WormBase gpi file: ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/gene_product_info/c_elegans.canonical_bioproject.current_development.gene_product_info.gpi.gz | ||
=== *Annotation Properties === | === *Annotation Properties === |
Revision as of 19:58, 20 July 2020
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 |
dependent_on | GOREL:0000004 |
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:
- PMID to WBPaper
- Relation text to gorel id
- Curators without orcids to GOC abbreviations
GPAD 2.0 column number | GPAD 2.0 column name | Action | UniProt Source File Example | WormBase Output File Example | Report on parsing failures |
---|---|---|---|---|---|
1 | Annotated entity* | Convert each UniProtKB: accession to a WBGene id using the latest WB gpi file | UniProtKB:G5ED58 | WB:WBGene00006925 | Yes |
2 | Negation | Leave as is | NOT | NOT | No |
3 | Qualifier* | Leave as is, except for BFO:0000050* | RO:0002327 | RO:0002327 | No |
4 | GO term ID | Leave as is | GO:0051306 | GO:0051306 | No |
5 | Reference* | Leave GO_REFs as is; map PMID or DOI to corresponding WBPaper id and add WBPaper id as a pipe-separated value | PMID:10978280 | PMID:10978280|WB:WBPaper00004310 | Yes |
6 | Evidence | Leave as is | ECO:0000314 | ECO:00000314 | No |
7 | With/From* | Leave as is, except for UniProtKB: accessions; for UniProtKB: accessions, try to map to a WBGene id using the latest WB gpi file; if UniProtKB: accession doesn't map to a WBGene id, then leave as is | UniProtKB:D9PTP8 | WB:WBGene00013354 | Yes - output a list of UniProtKB accessions that didn't map to a WBGene |
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 above. Otherwise, leave as is. Report on any relation text strings that didn't map to an id. | RO:0002233(WB:WBGene00000584) | ||
12 | Annotation properties* | Most will stay as is, except for history (see below). | contributor-id=https://orcid.org/0000-0002-1706-4196%7Ccomment=action:Updated by Kimberly Van Auken|model-state=deleted |
Annotated Entity
- Use latest WormBase gpi file to map UniProtKB accessions (column 1 in incoming GPAD file; column 9 in WB gpi file) to corresponding WBGene ID (column 2 in WB gpi file)
- Latest WormBase gpi file: ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/gene_product_info/c_elegans.canonical_bioproject.current_development.gene_product_info.gpi.gz
- For input values that include a '-digit', e.g. UniProtKB:P37806-1, strip the '-digit' for the purposes of mapping to a WBGene and add a comment in the Annotation properties field: comment=Original annotation made to whatever the full UniProtKB accession is. For example: comment=Original annotation made to UniProtKB:P37806-1.
Qualifiers
- For annotation lines that use BFO:0000050, check GO ID parentage. If GO:0032991 is a parent term, leave BFO:0000050. If GO:00032991 is not a parent term, change to RO:0001025.
References
- Map incoming doi or PMID to WBPaper id using the pap_identifier table.
With/From
- Use latest WormBase gpi file to map UniProtKB accessions (column 1 in incoming GPAD file; column 9 in WB gpi file) to corresponding WBGene ID (column 2 in WB gpi file)
- Latest WormBase gpi file: ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/gene_product_info/c_elegans.canonical_bioproject.current_development.gene_product_info.gpi.gz
*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
- History
- Group annotations by id, e.g. id=GOA:2113472118
- If more than one line with same id, check corresponding date field (column 9) for each line
- For most recent date of grouped annotations, leave line as is
- For earlier dates of grouped annotations, add 'model-state=deleted' to annotation properties field (column 12) by pipe-separating it from the last annotation properties entry
Final File for Import
- The final file for import will be a concatenated file of OA and Protein2GO GPAD files
- We'll need to make the file available for Dustin to pick up somewhere for the import.