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biothings / mygene.info

MyGene.info: A BioThings API for gene annotations
http://mygene.info
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add UMLS entries for proteins #79

Closed andrewsu closed 4 years ago

andrewsu commented 4 years ago

We currently have mappings to UMLS CUIs for genes (see #18). For example, on the entry for NOS3 http://mygene.info/v3/gene/4846, we have:

"umls": {
    "cui": "C1328053"
},

But since mygene effectively merges gene and protein objects, we should probably also add mappings to UMLS CUIs for proteins. For NOS3, that identifier would be https://uts.nlm.nih.gov/metathesaurus.html?cui=C0669365, which looks like it can be joined to our gene entries via Swiss-Prot identifiers in MRSAT.RRF (which I believe is a mapping file provided by UMLS)

image

(RefSeq also appears to be a common identifier that could be used for mapping...)

If that's all correct, then I'd suggest adding those mappings, perhaps in a structure like this:

"umls": {
    "cui": "C1328053",
    "protein_cui": "C0669365"
},
kevinxin90 commented 4 years ago

Updated in: 8dfc9240858ca5a5a196add8da6efd323051c88c. Also deployed to the production.

Example query: http://mygene.info/v3/gene/1017?fields=umls