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Conference Papers Year : 2023

Building a Corpus for Biomedical Relation Extraction of Species Mentions

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.
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Dates and versions

hal-04309226 , version 1 (29-11-2023)

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Oumaima El Khettari, Solen Quiniou, Samuel Chaffron. Building a Corpus for Biomedical Relation Extraction of Species Mentions. The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, Jul 2023, Toronto, Canada. pp.248-254, ⟨10.18653/v1/2023.bionlp-1.21⟩. ⟨hal-04309226⟩
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