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obophenotype / ncbitaxon

Build for NCBITaxon
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Use OMO for synonym type predicates #88

Closed cthoyt closed 7 months ago

cthoyt commented 9 months ago

Closes #87

This PR updates the RDF generation to use OMO terms, when available. It extends the predicates configuration dictionary at the top so that new OMO terms can be added in as they are minted. Currently, this PR switches 4 terms to using OMO:

Existing IRI New OMO IRI
http://purl.obolibrary.org/obo/ncbitaxon#acronym http://purl.obolibrary.org/obo/OMO_0003012
http://purl.obolibrary.org/obo/ncbitaxon#common_name http://purl.obolibrary.org/obo/OMO_0003003
http://purl.obolibrary.org/obo/ncbitaxon#misnomer http://purl.obolibrary.org/obo/OMO_0003007
http://purl.obolibrary.org/obo/ncbitaxon#misspelling http://purl.obolibrary.org/obo/OMO_0003006

There will have to be more detailed follow-up discussion if we want to complete the coverage of OMO on these synonyms.

cmungall commented 9 months ago

I think that's a good idea @jamesaoverton

cthoyt commented 9 months ago

I can make that announcement if you'd like. I would also include some more context about how we are working towards standardizing synoynms across other ontologies too, and similar things might pop up in the near future.

Edit: see the announcement

cthoyt commented 8 months ago

hi @anitacaron, is there anything else you'd like me to take care of to finish this PR? The OMO definitions now have the correct labels like in

OMO:0003000 a owl:AnnotationProperty ;
    rdfs:label "abbreviation"^^xsd:string ;
    oboInOwl:hasScope "oio:hasBroadSynonym"^^xsd:string ;
    rdfs:subPropertyOf oboInOwl:SynonymTypeProperty .
anitacaron commented 8 months ago

I'm still not sure about this axiom that is added to the OMO:0003000: oboInOwl:hasScope "oio:hasBroadSynonym"^^xsd:string ;

cthoyt commented 8 months ago

@anitacaron I also saw that and think there's something fishy, but I didn't want to make any changes to the existing functionality. I'm happy to make a second PR that makes this a proper reference to a IRI instead of a string if you think that will make assessing this PR easier

anitacaron commented 8 months ago

This axiom is added to the other annotations, original from NCBITaxon. Now, adding OMO as annotations should not include this.

cthoyt commented 8 months ago

So for OMO definitions it shouldn't have the scope added?

anitacaron commented 8 months ago

I think so. Someone else could confirm.

cthoyt commented 8 months ago

I think so. Someone else could confirm.

I removed the scope statement from OMO terms in 7f9fb51

cthoyt commented 8 months ago

@anitacaron would you please merge this? I think we're ready for a release, too.