Investigate missing MONDO xrefs

[caufieldjh]

Describe the bug

In reference to monarch-initiative/monarch-app#652 -
MONDO identifiers don't appear to have their corresponding OMIM IDs, or at least they don't end up in the Monarch KG.
They may go missing here or in KG-Phenio.

[matentzn]

Let me know what you find out. I would like to suggest that we should prefer the skos matches for populating the search index, but we will anyways drop all non-exact xrefs in future releases of Mondo, which means that the effect is the same.

[caufieldjh]

OK, it looks like MONDO classes still have their corresponding OMIM oboInOwl:hasDbXref and skos:exactMatch in phenio.owl, at least as of the most recent release (03-13-24).

Example for MONDO:0026765, the ID in the linked monarch-app issue:

<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0026765">
        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/monarch-initiative/mondo/issues/4521</obo:IAO_0000233>
        <oboInOwl:hasDbXref>OMIM:301045</oboInOwl:hasDbXref>
        <oboInOwl:hasExactSynonym>congenital disorder of glycosylation, type IIr, X-linked recessive</oboInOwl:hasExactSynonym>
        <oboInOwl:hasRelatedSynonym>CDG IIr</oboInOwl:hasRelatedSynonym>
        <oboInOwl:hasRelatedSynonym>CDG2R</oboInOwl:hasRelatedSynonym>
        <oboInOwl:hasRelatedSynonym>CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIr</oboInOwl:hasRelatedSynonym>
        <oboInOwl:id>MONDO:0026765</oboInOwl:id>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/mondo#inferred_rare"/>
        <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/mondo#rare"/>
        <rdfs:label>congenital disorder of glycosylation, type IIr</rdfs:label>
        <skos:exactMatch rdf:resource="https://omim.org/entry/301045"/>
    </rdf:Description>

I'm assuming that the linked issue here (monarch-initiative/mondo#4521) is unrelated as it's about name discrepancies and the map is still defined here as expected.

[caufieldjh]

Will look in KG-Phenio next.