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Open Access Research article

Towards classifying species in systems biology papers using text mining

Qi Wei1 and Nigel Collier12*

Author Affiliations

1 Department of Informatics, The Graduate University for Advanced Studies (Sokendai), 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo

2 National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo

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BMC Research Notes 2011, 4:32  doi:10.1186/1756-0500-4-32

Published: 4 February 2011



In recent years high throughput methods have led to a massive expansion in the free text literature on molecular biology. Automated text mining has developed as an application technology for formalizing this wealth of published results into structured database entries. However, database curation as a task is still largely done by hand, and although there have been many studies on automated approaches, problems remain in how to classify documents into top-level categories based on the type of organism being investigated. Here we present a comparative analysis of state of the art supervised models that are used to classify both abstracts and full text articles for three model organisms.


Ablation experiments were conducted on a large gold standard corpus of 10,000 abstracts and full papers containing data on three model organisms (fly, mouse and yeast). Among the eight learner models tested, the best model achieved an F-score of 97.1% for fly, 88.6% for mouse and 85.5% for yeast using a variety of features that included gene name, organism frequency, MeSH headings and term-species associations. We noted that term-species associations were particularly effective in improving classification performance. The benefit of using full text articles over abstracts was consistently observed across all three organisms.


By comparing various learner algorithms and features we presented an optimized system that automatically detects the major focus organism in full text articles for fly, mouse and yeast. We believe the method will be extensible to other organism types.