INCATools / INCATools/ontology-access-kit
Add PubTator implementation
- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
Description
This will implement ONLY TextAnnotator
https://www.ncbi.nlm.nih.gov/research/pubtator/api.html
Be sure to implement the throttle
Note that certain ID transformations will need to be transformed
Note: we may also want to extend the TextAnnotator API to accept PMIDs as well as texts; pubtator could then return cached results.
Contributor guide
Research direction
Start by locating the existing TextAnnotator API and reading the linked PubTator API documentation. Define the implementation boundary around TextAnnotator, then identify the required throttle behavior and ID transformations. Done means PubTator-backed text annotation is implemented with those requirements addressed; the PMID caching idea is explicitly outside this scope.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- api, backend
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100