Bacteria Biotope at BioNLP Open Shared Tasks 2019

Abstract

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 fulltext 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. c 2019 Association for Computational Linguistics.