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This article is part of the supplement: The Third BioCreative – Critical Assessment of Information Extraction in Biology Challenge

Open Access Research

Classifying protein-protein interaction articles using word and syntactic features

Sun Kim and W John Wilbur*

Author Affiliations

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

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BMC Bioinformatics 2011, 12(Suppl 8):S9  doi:10.1186/1471-2105-12-S8-S9

Published: 3 October 2011

Abstract

Background

Identifying protein-protein interactions (PPIs) from literature is an important step in mining the function of individual proteins as well as their biological network. Since it is known that PPIs have distinctive patterns in text, machine learning approaches have been successfully applied to mine these patterns. However, the complex nature of PPI description makes the extraction process difficult.

Results

Our approach utilizes both word and syntactic features to effectively capture PPI patterns from biomedical literature. The proposed method automatically identifies gene names by a Priority Model, then extracts grammar relations using a dependency parser. A large margin classifier with Huber loss function learns from the extracted features, and unknown articles are predicted using this data-driven model. For the BioCreative III ACT evaluation, our official runs were ranked in top positions by obtaining maximum 89.15% accuracy, 61.42% F1 score, 0.55306 MCC score, and 67.98% AUC iP/R score.

Conclusions

Even though problems still remain, utilizing syntactic information for article-level filtering helps improve PPI ranking performance. The proposed system is a revision of previously developed algorithms in our group for the ACT evaluation. Our approach is valuable in showing how to use grammatical relations for PPI article filtering, in particular, with a limited training corpus. While current performance is far from satisfactory as an annotation tool, it is already useful for a PPI article search engine since users are mainly focused on highly-ranked results.