Open Access Research article

U-Compare bio-event meta-service: compatible BioNLP event extraction services

Yoshinobu Kano12*, Jari Björne34, Filip Ginter3, Tapio Salakoski34, Ekaterina Buyko5, Udo Hahn5, K Bretonnel Cohen6, Karin Verspoor6, Christophe Roeder6, Lawrence E Hunter6, Halil Kilicoglu7, Sabine Bergler7, Sofie Van Landeghem8, Thomas Van Parys8, Yves Van de Peer8, Makoto Miwa9, Sophia Ananiadou9, Mariana Neves10, Alberto Pascual-Montano10, Arzucan Özgür1112, Dragomir R Radev1113, Sebastian Riedel14, Rune Sætre15, Hong-Woo Chun16, Jin-Dong Kim17, Sampo Pyysalo9, Tomoko Ohta18 and Jun'ichi Tsujii19

Author affiliations

1 Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan

2 National Institute of Informatics (NII), 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo, 101-8430, Japan

3 Department of Information Technology, University of Turku, Joukahaisenkatu 3-5, Turku, FI-20014, Finland

4 Turku Centre for Computer Science (TUCS), Joukahaisenkatu 3-5 B, Turku, FI-20520, Finland

5 Jena University Language & Information Engineering (JULIE) Lab, Friedrich-Schiller-Universität Jena, Fürstengraben 30, D-07743 Jena, Germany

6 Computational Bioscience Program, University of Colorado Denver School of Medicine, PO Box 6511, MS 8303, Aurora, CO 80045 USA

7 Department of Computer Science and Software Engineering, Concordia University, 1455 de Maisonneuve Blvd West, Montréal, QC, H3G 1M8, Canada

8 Department of Plant Systems Biology, VIB/Ghent University, Technologiepark 927, Ghent, B-9052, Belgium

9 The National Centre for Text Mining (NaCTeM) and School of Computer Science, the University of Manchester, Manchester, UK

10 National Center of Biotechnology-CSIC, C/Darwin 3, Campus de Cantoblanco, Madrid, 28049, Spain

11 Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA

12 Department of Computer Engineering, Bogazici University, 34342 Bebek, Istanbul, Turkey

13 School of Information, University of Michigan, Ann Arbor, MI 48109, USA

14 Department of Computer Science, University of Massachusetts Amherst, Massachusetts, USA

15 Department of Computer and Information Science (IDI), Norwegian University of Science and Technology (NTNU), Sem Sælands vei 7-9, Trondheim, NO-7491, Norway

16 Korea Institute of Science and Technology Information. 245 Daehangno, Yuseong-gu, Daejeon, 305-806, South Korea

17 Database Center for Life Science (DBCLS), Research Organization of Information and System, Faculty of Engineering Bldg. 12, the University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan

18 Department of Computer Science, University of Tokyo, Tokyo, Japan

19 Microsoft Research Asia, Building 2, No. 5 Dan Ling Street, Haidian District, Beijing, 100080 P.R.China

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Citation and License

BMC Bioinformatics 2011, 12:481  doi:10.1186/1471-2105-12-481

Published: 18 December 2011

First paragraph (this article has no abstract)

Bio-molecular event extraction from literature is recognized as an important task of bio text mining and, as such, many relevant systems have been developed and made available during the last decade. While such systems provide useful services individually, there is a need for a meta-service to enable comparison and ensemble of such services, offering optimal solutions for various purposes.