taxon:1 vs NCBITaxon:1 for goid response from ontology/term/ endpoint

[tmushayahama]

The API endpoint https://api.geneontology.org/api/ontology/term/NCBITaxon:1 returns id: taxon:1 instead of NCBITaxon:1

    {
       "goid":"taxon:1",
       "label":"root",
       ...
    }

However plugging taxon:1 as a closure to GOlr doesn't seem to work, but NCBITaxon:1 works

cc @sierra-moxon @kltm @vanaukenk

[cmungall]

It should be NCBITaxon:1

And to point out the obvious: it's not a GO ID. It's too late to fix this now I assume

[vanaukenk]

Noting from the 2024-06-13 workbenches call, that it's possible that other applications are expecting the existing value. We'll want to check on this before putting a fix in.

[kltm]

Also, as this has been there a while, it might be good to see if any of our widgets, etc., already code to this "bug".

[sierra-moxon]

debugging results:

• https://raw.githubusercontent.com/geneontology/go-site/master/metadata/db-xrefs.yaml uses taxon as the "database" for NCBITaxon identifiers. linkml/prefixmaps uses this file to make the prefixmap/context for the API, using the "database" field as the "prefix" in the prefix map and the "rdf_uriprefix" as the expansion prefix. (e.g. {"taxon":"http://purl.obolibrary.org/obo/NCBITaxon"})
  Then, the API uses this resulting context as the dictionary with which it does URI compression when returning results from our RDF endpoint (the RDF return for the 'id' being queried is in URI format).
  @kltm @cmungall -- should the db-xrefs.yaml 'database' parameter for NCBITaxon change from taxon to NCBITaxon?

• The API is returning as a goid from the API endpoint because the data structure of the return is hard coded as "goid."
  Which ontologies should a user querying this endpoint (noting that its getting data from the RDF endpoint) be able to query? (@kltm @tmushayahama)

[cmungall]

should the db-xrefs.yaml 'database' parameter for NCBITaxon change from taxon to NCBITaxon?

I think this is a good idea. We should also include a comment field indicating that taxon: is used in some file formats like GAF for legacy reasons.

[sierra-moxon]

Per discussion in developers' Slack, we will not change the hard coding of this endpoint to reflect its ability to search and return non-GO ontology identifiers.

The other half of this ticket is fixed in geneontology/go-site, but also has the potential to break other things.

So for now, this ticket won't be fixed.