Bacteria Biotope at BioNLP Open Shared Tasks 2019

Robert Bossy (1, 2) , Louise Deleger (1, 2) , Estelle Chaix (1) , Mouhamadou Ba (1, 2) , Claire Nédellec (1, 2)

1 MaIAGE - Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas]
2 Université Paris Saclay (COmUE)

This paper presents the fourth edition of the Bacteria Biotope task at BioNLP Open Shared Tasks 2019. The task focuses on the extraction of the locations and phenotypes of microorganisms from PubMed abstracts and full-text excerpts, and the characterization of these entities with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on biodiversity for fundamental research and applications in microbiology. The paper describes the different proposed subtasks, the corpus characteristics, and the challenge organization. We also provide an analysis of the results obtained by participants, and inspect the evolution of the results since the last edition in 2016.

Mots clés: intelligence artificielle; extraction d'information; biologie

Domaines: Intelligence artificielle [cs.AI]; Apprentissage [cs.LG]; Traitement du texte et du document; Microbiologie et Parasitologie

Robert Bossy, Louise Deleger, Estelle Chaix, Mouhamadou Ba, Claire Nédellec. Bacteria Biotope at BioNLP Open Shared Tasks 2019. 5th Workshop on BioNLP Open Shared Tasks BioNLP-OST@EMNLP-IJCNLP 2019, Association for Computational Linguistics, Jin-Dong Kim; Claire Nédellec; Robert Bossy; Louise Deléger, Nov 2019, Hong-Kong, Hong Kong SAR China. ⟨10.18653/v1/D19-5719⟩. ⟨hal-02437609⟩