This article is part of the supplement: Selected articles from the BioNLP Shared Task 2011

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BioNLP Shared Task - The Bacteria Track

Robert Bossy1, Julien Jourde1, Alain-Pierre Manine2, Philippe Veber1, Erick Alphonse2, Maarten van de Guchte3, Philippe Bessières1* and Claire Nédellec1*

Author Affiliations

1 Mathématique Informatique et Génome, Institut National de la Recherche Agronomique, INRA UR1077 - F78352 Jouy-en-Josas, France

2 PredictiveDB - 16, rue Alexandre Parodi - F75010 Paris, France

3 MICALIS, Institut National de la Recherche Agronomique, UMR1319 - F78352 Jouy-en-Josas, France

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BMC Bioinformatics 2012, 13(Suppl 11):S3  doi:10.1186/1471-2105-13-S11-S3

Published: 26 June 2012



We present the BioNLP 2011 Shared Task Bacteria Track, the first Information Extraction challenge entirely dedicated to bacteria. It includes three tasks that cover different levels of biological knowledge. The Bacteria Gene Renaming supporting task is aimed at extracting gene renaming and gene name synonymy in PubMed abstracts. The Bacteria Gene Interaction is a gene/protein interaction extraction task from individual sentences. The interactions have been categorized into ten different sub-types, thus giving a detailed account of genetic regulations at the molecular level. Finally, the Bacteria Biotopes task focuses on the localization and environment of bacteria mentioned in textbook articles.

We describe the process of creation for the three corpora, including document acquisition and manual annotation, as well as the metrics used to evaluate the participants' submissions.


Three teams submitted to the Bacteria Gene Renaming task; the best team achieved an F-score of 87%. For the Bacteria Gene Interaction task, the only participant's score had reached a global F-score of 77%, although the system efficiency varies significantly from one sub-type to another. Three teams submitted to the Bacteria Biotopes task with very different approaches; the best team achieved an F-score of 45%. However, the detailed study of the participating systems efficiency reveals the strengths and weaknesses of each participating system.


The three tasks of the Bacteria Track offer participants a chance to address a wide range of issues in Information Extraction, including entity recognition, semantic typing and coreference resolution. We found commond trends in the most efficient systems: the systematic use of syntactic dependencies and machine learning. Nevertheless, the originality of the Bacteria Biotopes task encouraged the use of interesting novel methods and techniques, such as term compositionality, scopes wider than the sentence.