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Bioinformatics. Jul 1, 2011; 27(13): i111–i119.
Published online Jun 14, 2011. doi:  10.1093/bioinformatics/btr214
PMCID: PMC3117364
Discovering and visualizing indirect associations between biomedical concepts
Yoshimasa Tsuruoka,1* Makoto Miwa,2,3,4 Kaisei Hamamoto,3 Jun'ichi Tsujii,3,4,5 and Sophia Ananiadou3,4
1School of Information Science, Japan Advanced Institute of Science and Technology (JAIST), Nomi, 2Department of Computer Science, The University of Tokyo, Tokyo, Japan, 3The National Centre for Text Mining (NaCTeM), 4School of Computer Science, The University of Manchester, Manchester, UK and 5Microsoft Research Asia, Beijing, China
* To whom correspondence should be addressed.
Motivation: Discovering useful associations between biomedical concepts has been one of the main goals in biomedical text-mining, and understanding their biomedical contexts is crucial in the discovery process. Hence, we need a text-mining system that helps users explore various types of (possibly hidden) associations in an easy and comprehensible manner.
Results: This article describes FACTA+, a real-time text-mining system for finding and visualizing indirect associations between biomedical concepts from MEDLINE abstracts. The system can be used as a text search engine like PubMed with additional features to help users discover and visualize indirect associations between important biomedical concepts such as genes, diseases and chemical compounds. FACTA+ inherits all functionality from its predecessor, FACTA, and extends it by incorporating three new features: (i) detecting biomolecular events in text using a machine learning model, (ii) discovering hidden associations using co-occurrence statistics between concepts, and (iii) visualizing associations to improve the interpretability of the output. To the best of our knowledge, FACTA+ is the first real-time web application that offers the functionality of finding concepts involving biomolecular events and visualizing indirect associations of concepts with both their categories and importance.
Availability: FACTA+ is available as a web application at, and its visualizer is available at
Contact: tsuruoka/at/
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