Building a Corpus for Biomedical Relation Extraction of Species Mentions

2023/06/14 by Oumaima El Khettari, Khettari, Oumaima El, Solen Quiniou +3 · 1 citation
Biochemistry, Genetics and Molecular Biology · Computer Science · #Advanced Text Analysis Techniques #Biomedical Text Mining and Ontologies #Computation and Language (cs.CL) #FOS: Computer and information sciences #Topic Modeling

paper · pdf · doi:10.48550/arxiv.2306.08403

openalex publication_date 2023/06/14 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Abstract

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.

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