Bugs in GPI 2.0 format - Githubissues

geneontology / pipeline

Declarative pipeline for the Gene Ontology.

https://build.geneontology.org/job/geneontology/job/pipeline/

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Bugs in GPI 2.0 format #380

Closed suzialeksander closed 4 months ago

suzialeksander commented 4 months ago

Looking at the new GPI 2.0, specifically sgd.gpi on skyhook:

[ ] Headers are missing required field: date-generated
[ ] Headers are missing required field: generated-by
[ ] Taxon field not using required NCBITaxon: prefix
[ ] Object types are text labels not ontology IDs

suzialeksander commented 4 months ago

Currently file looks like

!gpi-version: 2.0 SGD:S000006369 RHO1 GTP-binding protein of the rho subfamily of Ras-like small GTPases YPR165W|Rho family GTPase RHO1 protein taxon:559292
SGD:S000003211 ANK1 Cytoplasmic ankyrin repeat-containing protein YGL242C protein taxon:559292
SGD:S000002348 RBS1 Protein involved in assembly of the RNA Pol III complex YDL189W|[VTS1+] protein taxon:559292
SGD:S000028526 MCO10 Subunit l of the mitochondrial F1F0 ATP synthase YOR020W-A protein taxon:559292

kltm commented 4 months ago

@sierra-moxon From our conversation earlier, while I found the GO API ticket for taxon/NCBITaxon, I actually couldn't find an output one. Did I remember that wrong?

sierra-moxon commented 4 months ago

just part of the checklist above :) I can write a test and then check it off, instead? But the underlying problem with the taxon: syntax is the db-xrefs.yaml and is likely already fixed with the change we just committed to the go-site db-xrefs.yaml file (now percolating through linkml/prefixmaps and ontobio, etc.)

kltm commented 4 months ago

Cheers--I was probably conflating something with https://github.com/geneontology/go-fastapi/issues/95