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This article is part of the supplement: The BioCreative II - Critical Assessment for Information Extraction in Biology Challenge

Open Access Software

Introducing meta-services for biomedical information extraction

Florian Leitner1*, Martin Krallinger1, Carlos Rodriguez-Penagos1, Jörg Hakenberg23, Conrad Plake2, Cheng-Ju Kuo45, Chun-Nan Hsu5, Richard Tzong-Han Tsai6, Hsi-Chuan Hung5, William W Lau7, Calvin A Johnson7, Rune Sætre8, Kazuhiro Yoshida8, Yan Hua Chen9, Sun Kim10, Soo-Yong Shin10, Byoung-Tak Zhang10, William A Baumgartner11, Lawrence Hunter11, Barry Haddow12, Michael Matthews12, Xinglong Wang12, Patrick Ruch13, Frédéric Ehrler14, Arzucan Özgür15, Güneş Erkan15, Dragomir R Radev15, Michael Krauthammer16, ThaiBinh Luong17, Robert Hoffmann18, Chris Sander19 and Alfonso Valencia1*

Author Affiliations

1 Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), C/Melchor F. Almagro 3, 28029 Madrid, Spain

2 Bioinformatics group, Biotechnological Centre, Technical University Dresden, Tatzberg 47-51, 01307 Dresden, Germany

3 Humboldt Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany

4 Institute of Bioinformatics, National Yang-Ming University, No. 155, Sec. 2, Linong St., Beitou District, Taipei City 112, Taiwan

5 Institute of Information Science, Academia Sinica, No.128, Sec. 2, Academia Rd., Nangang District, Taipei City 115, Taiwan

6 Department of Computer Science and Engineering, Yuan Ze University, 135 Yuan-Tung Rd., Chung-Li, Taoyuan, R.O.C., 32003, Taiwan

7 Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA

8 Department of Computer Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, 113-0033 Tokyo, Japan

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

10 Biointelligence Laboratory, School of Computer Science and Engineering, Seoul National University, Seoul 151-744, Korea

11 Center for Computational Pharmacology, University of Colorado School of Medicine, P.O. Box 6511, Mail Stop 8303, Aurora, CO 80045-0511, USA

12 School of Informatics, University of Edinburgh, 2 Buccleuch Place, Edinburgh, EH8 9LW, UK

13 Text Mining Group, Medical Informatics Service, University and Hospitals of Geneva, 24 Micheli du Crest, 1201 Geneva, Switzerland

14 Artificial Intelligence Group, University of Geneva, 7 route de Drize, 1227 Carouge, Switzerland

15 Department of Electrical Engineering and Computer Science, University of Michigan, 2260 Hayward Street, Ann Arbor, MI 48109, USA

16 Department of Pathology, Yale University School of Medicine, 300 Cedar Street, TAC 309, New Haven, CT 06520-8023, USA

17 Program for Computational Biology and Bioinformatics, Yale University, Suite 501, 300 George Street, New Haven, CT 06520-8084, USA

18 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), The Stata Center Building 32, 32 Vassar Street, Cambridge, MA 02139, USA

19 Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA

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Genome Biology 2008, 9(Suppl 2):S6  doi:10.1186/gb-2008-9-s2-s6

Published: 1 September 2008

Abstract

We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/ webcite). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations.