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

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matentzn opened this issue Feb 13, 2024 · 1 comment · Fixed by #18
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Add HPO<->UMLS and HPO<->MeSH mapping to MedGen release #16

matentzn opened this issue Feb 13, 2024 · 1 comment · Fixed by #18
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@matentzn
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Context here: obophenotype/human-phenotype-ontology#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 joeflack4 self-assigned this Feb 13, 2024
@joeflack4 joeflack4 changed the title Add HPO - UMLS and HPO - MeSH mapping to medgen release Add HPO::UMLS and HPO::MeSH mapping to medgen release Feb 13, 2024
@joeflack4 joeflack4 changed the title Add HPO::UMLS and HPO::MeSH mapping to medgen release Add HPO<->UMLS and HPO<->MeSH mapping to medgen release Feb 13, 2024
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joeflack4 commented Feb 13, 2024

Yes, it seems doable in less than 2 hours. I just spent 20 minutes reading up on this, had to skip most of obophenotype/human-phenotype-ontology#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 monarch-initiative/mondo-ingest#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.

@joeflack4 joeflack4 changed the title Add HPO<->UMLS and HPO<->MeSH mapping to medgen release Add HPO<->UMLS and HPO<->MeSH mapping to MedGen release Mar 13, 2024
@joeflack4 joeflack4 linked a pull request Mar 23, 2024 that will close this issue
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