BENT: Biomedical Entity Annotator

BENT: Biomedical Entity Annotator

Python Library for Named Entity Recognition (NER) and Linking (NEL) in the biomedical domain.

NER models are based on PubMedBERT and a post-processing rule-based module. NEL model is a graph-based approach based on the Personalized PageRank algorithm and Information content.

Python package

Github repository

Contents:

• Installation
• Usage
• Documentation
  • annotate

Citation:

[1]

Pedro Ruas and Francisco M. Couto. Nilinker: attention-based approach to nil entity linking. Journal of Biomedical Informatics, 132:104137, 2022. URL: https://www.sciencedirect.com/science/article/pii/S1532046422001526, doi:https://doi.org/10.1016/j.jbi.2022.104137.

Indices and tables

• Index

• Search Page