The omim.sssom.tsv file contains MONDO<->OMIM mappings to obsolete OMIM terms

[twhetzel]

In reviewing a feature build in the mondo-ingest repo, I came across a line where it shows a Mondo term mapped to an obsoleted OMIM term. I see that the omim.owl file has the OMIM term obsoleted and maintains the skos:exactMatch to the Mondo term and in Mondo it still has a database_cross_reference (or xref) to this OMIM term. Why are obsolete OMIM terms being included in the SSSOM file? For 'MOVED TO' OMIM entries, why does the omim code not apply the information to the new OMIM term? Since this OMIM edit occurred on October 15, 2024, was this too recent for our pipelines to catch this?

The mapping also shows up in src/ontology/lexmatch/mondo-only/unmapped_omim_mondo.tsv . It does show up in some other files as deprecated, e.g. docs/reports/mapped_deprecated_omim.md and src/ontology/reports/omim_mapped_deprecated_terms.robot.template.tsv (these are all files in the mondo-ingest repo).