Bacteria Biotope 2019

Extracting information about microbial biotopes and phenotypes

Bacteria Biotope at BioNLP-OST 2019

The Bacteria Biotope (BB) Task is part of the BioNLP Open Shared Tasks (BioNLP-OST: and meets the BioNLP-OST standards of quality, originality and data formats.

Manually annotated data is provided for training, development and evaluation of information extraction methods. Tools for the detailed evaluation of system outputs will be available for participants. Support in performing linguistic processing will be provided to the participants in the form of analyses created by various state-of-the art tools on the dataset texts.

Participation to the task is open to the academia, industry, and all other interested parties.

The results of the BB Task will be presented at the BioNLP-OST workshop which is collocated with EMNLP-IJCNPL in Hong-Kong. Participating teams will be invited to submit their system description for publication in the proceedings of the workshop.


  • April 18: Partial training data release
  • May 29: Full training data release
  • July 22-29: Test data release and evaluation
  • August 19: Workshop paper submission
  • Sept. 16: Paper acceptance notification
  • Sept. 30: Camera-ready papers due
  • Nov. 3 or 4: BioNLP-OST workshop


Biology and bioinformatics projects produce huge amounts of heterogeneous information about the microbial strains that have been experimentally identified in a given environment (habitat), and theirs properties (phenotype). These projects include applied microbiology domain (food safety), health sciences and waste processing. Knowledge about microbial diversity is critical for studying in depth the microbiome, the interaction mechanisms of bacteria with their environment from genetic, phylogenetic and ecology perspectives.

A large part of the information is expressed in free text in large sets of scientific papers, web pages or databases. Thus, automatic systems are needed to extract the relevant information. The BB task aims to encourage the development of such systems.

BB Task Goal

The BB Task is an information extraction task involving entity recognition, entity normalization and relation extraction.

The BB Task consists in recognizing mentions of microorganisms and microbial biotopes and phenotypes in scientific and textbook text, normalizing these mentions according to domain knowledge resources (a taxonomy and an ontology), and extracting relations between them.

It is the new edition of the Bacteria Biotope task previously run at BioNLP Shared Task 2016, 2013 and 2011. This year, the task has been extended to include new entity and relation types and new documents.

Details about the task are given in the Task Description page.