Building a Corpus for Biomedical Relation Extraction of Species Mentions
Oumaima El Khettari Solen Quiniou Samuel Chaffron
We present a manually annotated corpus, Species-Species Interaction, for
extracting meaningful binary relations between species, in biomedical texts, at
sentence level, with a focus on the gut microbiota. The corpus leverages
PubTator to annotate species in full-text articles after evaluating different
Named Entity Recognition species taggers. Our first results are promising for
extracting relations between species using BERT and its biomedical variants.