GOTerm extending OntologyTerm in core sources

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GOTerm extending OntologyTerm in core sources

Sam Hokin-3
Is there any strong reason why the core GO-related loaders go-annotation, go, interpro-go, psi-complexes and uniprot use GOTerm,
GOAnnotation rather than the superclass OntologyTerm and OntologyAnnotation? I realize that certain applications (like, perhaps,
FlyMine) may want to extend Ontology* for GO terms, but I'm not seeing a _core_ reason for doing so.

I'm leaning toward loading GO as just another feature annotation ontology (in addition to PFAM, PANTHER, etc.) so I'd like to hear a
strong reason to leave GO terms on their own special island. Maybe the enrichment widget requires a standalone class? That seems
fixable, if so.
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Re: GOTerm extending OntologyTerm in core sources

Julie Sullivan-2
Hi Sam!

I think that's because GOAnnotation came first before
OntologyAnnotation, so no strong reason.

It's more "correct" to use OntologyAnnotation, as you suggest! :)

We did some work a few releases ago to migrate some GOAnnotation fields
up to OntologyAnnotation as well.

Cheers
Julie

On 06/05/2019 19:14, Sam Hokin wrote:

> Is there any strong reason why the core GO-related loaders
> go-annotation, go, interpro-go, psi-complexes and uniprot use GOTerm,
> GOAnnotation rather than the superclass OntologyTerm and
> OntologyAnnotation? I realize that certain applications (like, perhaps,
> FlyMine) may want to extend Ontology* for GO terms, but I'm not seeing a
> _core_ reason for doing so.
>
> I'm leaning toward loading GO as just another feature annotation
> ontology (in addition to PFAM, PANTHER, etc.) so I'd like to hear a
> strong reason to leave GO terms on their own special island. Maybe the
> enrichment widget requires a standalone class? That seems fixable, if so.
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
_______________________________________________
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