Building a Corpus for Biomedical Relation Extraction of Species Mentions

Oumaima El Khettari, Solen Quiniou, Samuel Chaffron

Abstract: We present a manually annotated new corpus, Species-Species Interaction (SSI), 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 NER species taggers. Our first results are promising for extracting relations between species using BERT and its biomedical variants.