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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Add GHA QC for subsets YAML schema #27399

Open kltm opened 3 months ago

kltm commented 3 months ago

We now have a YAML for all subsets, (https://github.com/geneontology/go-ontology/blob/master/src/ontology/subsets/subsets.schema.yaml), but we need to add QC checking for this.

From @cmungall , we can use linkml for this, and port it in like schemauto import-kwalify my/schema/personinfo.kwalify.yaml

kltm commented 3 months ago

@pgaudet GHA for metadata is a requirement for the software side, so adding to project.

kltm commented 2 weeks ago

@pgaudet I'll need some additional info on the PR (https://github.com/geneontology/go-ontology/pull/28196) to bring the metadata into line with the schema.

pgaudet commented 2 weeks ago

hi @kltm

In go_subsets_metadata.yaml, goslim_virus has two roles; the schema requires a single role

OK, I can we have a subset have two roles? can I duplicate the entry? I would rather not create a copy of the subset itself. Or is this something we can change in the metadata spaces? I couldn't see that it was a single-value field.

In go_subsets_metadata.yaml, goslim_goa needs the additional metadata (like contact, role) to conform with the schema, even though it is obsolete; this can be cribbed from the other obsolete subsets?

fixed. However I noticed that the subset is archived on the cvs repository, which is offline: http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/GO_slims/archived_GO_slims/goslim_goa.2002?rev=1.4;content-type=text%2Fplain

Do we have a copy anywhere? Should we write that it's unavailable?

kltm commented 2 weeks ago

@pgaudet