INCATools / INCATools/ontology-access-kit
Include UMLS implementation
- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
Description
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/
Contributor guide
Research direction
Start by inspecting src/oaklib/implementations/umls and the BasicOntologyInterface and TextAnnotator interfaces. Read the UMLS REST API documentation and evaluate the referenced umls-api and pymetamap projects for Python 3 compatibility. Done means the UMLS implementation scope is resolved and the selected lookup and/or MetaMap capabilities are implemented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- api, backend
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100