INCATools / INCATools/ontology-access-kit

Include UMLS implementation

Open
#187 2 comments 0 reactions 0 assignees View on GitHub
enhancement
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

Open the contributing 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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.