Bacteria Biotope at BioNLP Open Shared Tasks 2019

Robert Bossy, Louise Deléger, Estelle Chaix, Mouhamadou Ba, Claire Nédellec


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 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.
Anthology ID:
D19-5719
Volume:
Proceedings of the 5th Workshop on BioNLP Open Shared Tasks
Month:
November
Year:
2019
Address:
Hong Kong, China
Venue:
BioNLP
SIG:
Publisher:
Association for Computational Linguistics
Note:
Pages:
121–131
Language:
URL:
https://aclanthology.org/D19-5719
DOI:
10.18653/v1/D19-5719
Bibkey:
Cite (ACL):
Robert Bossy, Louise Deléger, Estelle Chaix, Mouhamadou Ba, and Claire Nédellec. 2019. Bacteria Biotope at BioNLP Open Shared Tasks 2019. In Proceedings of the 5th Workshop on BioNLP Open Shared Tasks, pages 121–131, Hong Kong, China. Association for Computational Linguistics.
Cite (Informal):
Bacteria Biotope at BioNLP Open Shared Tasks 2019 (Bossy et al., BioNLP 2019)
Copy Citation:
PDF:
https://aclanthology.org/D19-5719.pdf
Data
BBBB-norm-habitatBB-norm-phenotype