Include UMLS implementation - Githubissues

INCATools / ontology-access-kit

Ontology Access Kit: A python library and command line application for working with ontologies

https://incatools.github.io/ontology-access-kit/

Apache License 2.0

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Include UMLS implementation #187

Open cmungall opened 2 years ago

cmungall commented 2 years ago

Fill in this stub dir: https://github.com/INCATools/ontology-access-kit/tree/main/src/oaklib/implementations/umls

We may want to have this implementation wrap two different aspects of UMLS

lookups, implementing BasicOntologyInterface e.g via API https://documentation.uts.nlm.nih.gov/rest/home.html
metamap, implementing TextAnnotator

Some existing python code we could wrap

https://pypi.org/project/umls-api/
- seems quite barebones
https://github.com/AnthonyMRios/pymetamap
- seems quite old, is it even python3?
- https://gweissman.github.io/post/using-metamap-with-python-to-access-the-umls-metathesaurus-a-quick-start-guide/

matentzn commented 2 years ago

Awesome!!!

cthoyt commented 2 years ago

https://github.com/cthoyt/umls_downloader automates getting the source data