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Open Access Highly Accessed Open Badges Research article

A realistic assessment of methods for extracting gene/protein interactions from free text

Renata Kabiljo1*, Andrew B Clegg2 and Adrian J Shepherd1

Author affiliations

1 School of Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London WC1E 7HX UK

2 Research Department of Structural and Molecular Biology and Institute of Structural and Molecular Biology, University College London, Gower St, London, WC1E 6BT UK

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Citation and License

BMC Bioinformatics 2009, 10:233  doi:10.1186/1471-2105-10-233

Published: 28 July 2009



The automated extraction of gene and/or protein interactions from the literature is one of the most important targets of biomedical text mining research. In this paper we present a realistic evaluation of gene/protein interaction mining relevant to potential non-specialist users. Hence we have specifically avoided methods that are complex to install or require reimplementation, and we coupled our chosen extraction methods with a state-of-the-art biomedical named entity tagger.


Our results show: that performance across different evaluation corpora is extremely variable; that the use of tagged (as opposed to gold standard) gene and protein names has a significant impact on performance, with a drop in F-score of over 20 percentage points being commonplace; and that a simple keyword-based benchmark algorithm when coupled with a named entity tagger outperforms two of the tools most widely used to extract gene/protein interactions.


In terms of availability, ease of use and performance, the potential non-specialist user community interested in automatically extracting gene and/or protein interactions from free text is poorly served by current tools and systems. The public release of extraction tools that are easy to install and use, and that achieve state-of-art levels of performance should be treated as a high priority by the biomedical text mining community.