INCATools / INCATools/ontology-access-kit

Add PubTator implementation

Open
#396 0 comments 1 reaction 0 assignees View on GitHub
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

Open the contributing 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

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.