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Remove duplicate OMA references #278

Open cthoyt opened 2 years ago

cthoyt commented 2 years ago

In the Ontology Quality Assessment, I found that there was an unknown prefix oma (see https://cthoyt.com/oquat/unknowns/prefix/oma). This apparently only appears in definition xrefs in PRO entries that shadow UniProt identifiers - it's not really an appropriate use of this field, and even further, it just duplicates the identifier already available in the term's URI itself as well as the dbxref to uniprot.

For example PR pages that shadow UniProt identifiers like https://proconsortium.org/app/entry/PR:Q01112 have links to OMA as if they're xrefs.

Related: I also added OMA as a provider in the Bioregistry in https://github.com/biopragmatics/bioregistry/pull/433

nataled commented 2 years ago

The links to OMA 'as if they're xrefs' is--if I understand what you're seeing correctly--a long-standing failing on the part of the OBO-to-OWL conversion. They are intended as links to evidence for orthology. As such, they are not the same as UniProtKB xrefs (in fact, only those PR terms with such evidence have the OMA link, and these are a subset of PR terms with UniProtKB xrefs).

Thank you for the addition of OMA to the Bioregistry.