Connecting UMLS CUIs to Wikidata using openly available resources.
cui_wiki.json file obtained from https://github.com/afshinrahimi/wikiumls/blob/master/data/cui_wiki.json, originally from this publication:
https://www.wikidata.org/wiki/Q105870539
It has, however, a large number of incorrect matches. The taxa seem to have a high score, so one way to go is to subset the dataset just for the taxa on Wikidata.
cui_wikidata_from_mesh.json obtained with parse_umls_to_wikidata.py on the output of
grep '|MSH|' MRCONSO.RRF | awk -F '|' '$7=="Y"{print $1 "|" $14 }' | sort -u > mesh.txt
On UMLS' 2023 MRCONSO.RRF release
Other possible sources of UMLS to Wikidata matching:
- https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ICD10CM/index.html
- https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/GO/index.html
- https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HGNC/index.html
- https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ORPHANET/index.html
- https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/FMA/index.html
- https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/NCBI/index.html
Other sources on UMLS are listed on nlm.nih.gov/research/umls/sourcereleasedocs/index.html