Ensure that the relation map used by ontobio in sync with the current state of the ontology

[kltm]

This stems from #397

Basically, the mapping of relation labels to IDs is hard-coded in ontobio and we want to fix that.

https://github.com/biolink/ontobio/blob/4abdd9fb83c0789f3f7400170969431f528c82a1/ontobio/rdfgen/relations.py#L128
https://github.com/biolink/ontobio/blob/4abdd9fb83c0789f3f7400170969431f528c82a1/ontobio/io/gafparser.py#L522
https://github.com/biolink/ontobio/blob/4abdd9fb83c0789f3f7400170969431f528c82a1/ontobio/model/association.py#L445

The most recent conversation is:

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@pgaudet

The thing is, this relation is valid in RO, and the inference chain is correct. However we have decided that we dont want to use this in GO. I had added subsets in RO to express which relations were valid for GO (annotations, extensions, ontology...) but @cmungall remarked that we shouldn't have information specific to a project in a 'general'/broader application ontology, which makes sense.

My question is, where can we put this information, since RO is not sufficient? I see a few options:

• We trust RO and deepen relations as appropriate (but that would be reverting many changes that we asked curators to fix)
• Use GOREL (which seems to be unavoidable?)
• Use ShEX.

There must be a documented source of truth for what's hard-coded in the code.

Thanks, Pascale

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@sierra-moxon

For my understanding, is GOREL curated or otherwise automatically maintained as the source of truth for relations applicable in GO? From this file: https://github.com/geneontology/go-ontology/blob/master/src/ontology/extensions/gorel.obo I see that all terms in GOREL have an xref to RO. Can I use that with confidence to do this same work in the code (but use the GOREL ontology instead of the map in the code)? If that is the case, I don't think it would be terribly hard to convert.

[kltm]

I would note that while we should have a fix in, this is also a "GORULE" and is something that Alex may be taking care of wrt end user files.
As well, I was under the impression that we are getting rid of GOREL long-term, so wouldn't that just be deferring the issue (e.g. : geneontology/go-ontology#19497)?

[pgaudet]

this is also a "GORULE"

Is this right ? AFAIK we dont 'fix' extensions. But we could say we delete non-compliant annotations (which is to obad, because the curator never made that statement)