manual mapping of non-drug interventions in GTRx

andrewsu commented 2 years ago

In https://github.com/biothings/pending.api/issues/62, we are loading GTRx, a database of diseases and their corresponding treatments. However, we decided to only load drug treatments, ignoring the treatments that are surgical procedures, dietary changes, and other non-pharmaceutical interventions. We made this choice because drug treatments are the only interventions with mappings to an external identifier (INXIGHT).

This issue tracks a proposal by @colleenXu to manually map non-pharmaceutical interventions to appropriate vocabularies (e.g., UMLS, MESH).

colleenXu commented 2 years ago

Ideas:

Name Resolver service https://name-resolution-sri.renci.org/docs#/lookup/lookup_curies_lookup_post
MESH https://meshb.nlm.nih.gov/
NCIT. Is it https://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI%20Metathesaurus&type=synonym&code=C0085430 ?
UMLS. some related old notes:

Procedures? UMLS IDs like "cord blood transplantation" (not many cross-maps) and "liver transplant" (has some some cross-maps) https://athena.ohdsi.org/search-terms/terms/2002365 for cord blood transplantation, also doesn't have cross-mapping…

colleenXu commented 7 months ago

@everaldorodrigo @newgene @andrewsu

This issue may also be nice to address?

biothings / pending.api

manual mapping of non-drug interventions in GTRx #72