Create a complete UMLS-OMIM SSSOM mapping file

monarch-initiative / omim

Data ingest pipeline for OMIM.

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Closed matentzn closed 2 years ago

matentzn commented 2 years ago

Covering all diseases in OMIM.

See #44, should be attached to release.

joeflack4 commented 2 years ago

This sounds like it should be easy to do with what I have available.

For my input, I'd use the latest omim.ttl from our OMIM ingest.

That file already has mappings to UMLS in the form of: oboInOwl:hasDbXref UMLS:<code>

For the UMLS prefix, the one we've been using and which I'll continue to use will be: http://linkedlifedata.com/resource/umls/id/

If any of this sounds incorrect, just let me know.

matentzn commented 2 years ago

instead of hasDbXref, for the sssom file, use skos:exactMatch.
For Mondo related work, lets consolidate our prefixes here: https://github.com/monarch-initiative/mondo/blob/master/src/ontology/metadata/mondo.sssom.config.yml

joeflack4 commented 2 years ago

Got it!

joeflack4 commented 2 years ago

Results in latest release. I think I still need to split the file, though: https://github.com/monarch-initiative/omim/releases/tag/latest