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monarch-initiative / medgen

MedGen ingest.
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Add HPO<->UMLS and HPO<->MeSH mapping to MedGen release #16

Closed matentzn closed 7 months ago

matentzn commented 9 months ago

Context here: https://github.com/obophenotype/human-phenotype-ontology/issues/9750

We need the two mappings as SSSOM files, we will serve them throught the Monarch Mapping Commons.

@joeflack4 give me a sense if you will be able to do this quickly or if this will take you more than 1 or 2 hours. If the former, I would suggest to couple this issue with #15 and do them both at once. @twhetzel do you agree? Both these issues require processing of the same file (MedgenIDMappings). If the latter, i.e. it will likely take you more than 2 hours, please let me know before you attempt to tackle this.

joeflack4 commented 9 months ago

Yes, it seems doable in less than 2 hours. I just spent 20 minutes reading up on this, had to skip most of https://github.com/obophenotype/human-phenotype-ontology/issues/9750, it's more than I need to know. I lost my MedGen environment when my PC died so I had to set a few things up. It sounds like this one can come before #15 and before https://github.com/monarch-initiative/mondo-ingest/pull/412 then. I should be able to start on this tomorrow or Thursday. Edit: I heard a priority update on this; will do this in between my two ICD11 PRs.