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. 2012 Jun 26;13 Suppl 11(Suppl 11):S3.
doi: 10.1186/1471-2105-13-S11-S3.

BioNLP Shared Task--The Bacteria Track

Robert Bossy  1 , Julien Jourde, Alain-Pierre Manine, Philippe Veber, Erick Alphonse, Maarten van de Guchte, Philippe Bessières, Claire Nédellec
Affiliations

BioNLP Shared Task--The Bacteria Track

Robert Bossy et al. BMC Bioinformatics. .

Abstract

Background: 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.

Results: 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.

Conclusions: 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 common 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.

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Figures

Figure 1
Figure 1
Example of gene renaming relations.
Figure 2
Figure 2
Example of gene interaction relations.
Figure 3
Figure 3
Common types of renaming sentences.
Figure 4
Figure 4
Example of bacteria biotopes relations.
Figure 5
Figure 5
Example of a coreference.
Figure 6
Figure 6
Examples of commonly missed gene interactions.
See this image and copyright information in PMC

References

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