BELB: a biomedical entity linking benchmark.

ABSTRACT:

Motivation

Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base (KB). It plays a vital role in information extraction pipelines for the life sciences literature. We review recent work in the field and find that, as the task is absent from existing benchmarks for biomedical text mining, different studies adopt different experimental setups making comparisons based on published numbers problematic. Furthermore, neural systems are tested primarily on instances linked to the broad coverage KB UMLS, leaving their performance to more specialized ones, e.g. genes or variants, understudied.

Results

We therefore developed BELB, a biomedical entity linking benchmark, providing access in a unified format to 11 corpora linked to 7 KBs and spanning

SUBMITTER: Garda S 

PROVIDER: S-EPMC10681865 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature