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Bioinformatics Advance Access originally published online on May 4, 2009
Bioinformatics 2009 25(15):1997-1998; doi:10.1093/bioinformatics/btp289
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

U-Compare: share and compare text mining tools with UIMA

Yoshinobu Kano 1,*, William A. Baumgartner, Jr 2, Luke McCrohon 1, Sophia Ananiadou 3,4, K. Bretonnel Cohen 2, Lawrence Hunter 2 and Jun'ichi Tsujii 1,3,4

1 Department of Computer Science, University of Tokyo Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033 Japan, 2 Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA, 3 School of Computer Science, University of Manchester and 4 National Centre for Text Mining, 131 Princess St., M1 7DN, UK

* To whom correspondence should be addressed.


  Abstract

Summary: Due to the increasing number of text mining resources (tools and corpora) available to biologists, interoperability issues between these resources are becoming significant obstacles to using them effectively. UIMA, the Unstructured Information Management Architecture, is an open framework designed to aid in the construction of more interoperable tools. U-Compare is built on top of the UIMA framework, and provides both a concrete framework for out-of-the-box text mining and a sophisticated evaluation platform allowing users to run specific tools on any target text, generating both detailed statistics and instance-based visualizations of outputs. U-Compare is a joint project, providing the world's largest, and still growing, collection of UIMA-compatible resources. These resources, originally developed by different groups for a variety of domains, include many famous tools and corpora. U-Compare can be launched straight from the web, without needing to be manually installed. All U-Compare components are provided ready-to-use and can be combined easily via a drag-and-drop interface without any programming. External UIMA components can also simply be mixed with U-Compare components, without distinguishing between locally and remotely deployed resources.

Availability: http://u-compare.org/

Contact: kano{at}is.s.u-tokyo.ac.jp

Associate Editor: Jonathan Wren

Received on February 7, 2009; revised on March 26, 2009; accepted on April 24, 2009

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