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Bioinformatics Advance Access first published online on February 22, 2005
This version published online on March 3, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti338
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received November 19, 2004
Revised February 13, 2005
Accepted February 17, 2005

Article

MaSTerClass: a case-based reasoning system for the classification of biomedical terms

Irena Spasic 1*, Sophia Ananiadou 2, and Jun-ichi Tsujii 3

1 School of Chemistry, The University of Manchester, Sackville Street, PO Box 88, Manchester, M60 1QD, UK
2 School of Computing, Science and Engineering, The University of Salford, The Crescent, Salford, M5 4WT, UK
3 Faculty of Information Science and Technology, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan

* To whom correspondence should be addressed.
Irena Spasic, E-mail: i.spasic{at}manchester.ac.uk


  Abstract

Motivation: The sheer volume of textually described biomedical knowledge exerts the need for natural language processing (NLP) applications in order to allow flexible and efficient access to relevant information. Specialised semantic networks (such as biomedical ontologies, terminologies or semantic lexicons) can significantly enhance these applications by supplying the necessary terminological information in a machine-readable form. Due to the explosive growth of bio-literature, new terms (representing newly identified concepts or variations of the existing terms) may not be explicitly described within the network and hence cannot be fully exploited by NLP applications. Linguistic and statistical clues can be used to extract many new terms from free text. The extracted terms still need to be correctly positioned relative to other terms in the network. Classification as a means of semantic typing represents the first step in updating a semantic network with new terms.

Results: The MASTERCLASS system implements the case-based reasoning methodology for the classification of biomedical terms.

Availability: MASTERCLASS is available at http://www.cbr-masterclass.org. It is distributed under an open source licence for educational and research purposes. The software requires Java, JWDSP, Ant, MySQL and X-hive to be installed and licences obtained separately where needed.


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