Overview of the bacteria biotope task at BioNLP shared task

Louise Deleger (1) , Robert Bossy (1) , Estelle Chaix (1) , Mouhamadou Ba (1) , Arnaud Ferré (1) , Philippe Bessieres (1) , Claire Nédellec (1)

1 MaIAGE - Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas]

This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2016, which follows the previous 2013 and 2011 editions. The task focuses on the extraction of the locations (biotopes and geographical places) of bacteria from PubMe abstracts and the characterization of bacteria and their associated habitats with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on bacteria habitats for fundamental research and applications in microbiology. The paper describes the different proposed subtasks, the corpus characteristics, the challenge organization, and the evaluation metrics. We also provide an analysis of the results obtained by participants.

Mots clés: information extraction; shared task; corpus; microbiology; ontology; biotope

Domaines: Sciences du Vivant [q-bio]

Louise Deleger, Robert Bossy, Estelle Chaix, Mouhamadou Ba, Arnaud Ferré, et al.. Overview of the bacteria biotope task at BioNLP shared task. BioNLP Shared Task, Aug 2016, Berlin, Germany. pp.101. ⟨hal-01455857⟩