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

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Abstract
Background: 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. Results: We have integrated nine event extraction systems in the U-Compare framework, making them inter-compatible and interoperable with other U-Compare components. The U-Compare event meta-service provides various meta-level features for comparison and ensemble of multiple event extraction systems. Experimental results show that the performance improvements achieved by the ensemble are significant. Conclusions: While individual event extraction systems themselves provide useful features for bio text mining, the U-Compare meta-service is expected to improve the accessibility to the individual systems, and to enable meta-level uses over multiple event extraction systems such as comparison and ensemble.
Keywords
INFORMATION EXTRACTION, text-mining, BioNLP, event extraction, meta-service, CORPUS

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Citation

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MLA
Kano, Yoshinobu, et al. “U-Compare Bio-Event Meta-Service : Compatible BioNLP Event Extraction Services.” BMC BIOINFORMATICS, vol. 12, 2011.
APA
Kano, Y., Bjorne, J., Ginter, F., Salakoski, T., Buyko, E., Hahn, U., … Tsujii, J. (2011). U-Compare bio-event meta-service : compatible BioNLP event extraction services. BMC BIOINFORMATICS, 12.
Chicago author-date
Kano, Yoshinobu, Jari Bjorne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, Kevin Cohen, et al. 2011. “U-Compare Bio-Event Meta-Service : Compatible BioNLP Event Extraction Services.” BMC BIOINFORMATICS 12.
Chicago author-date (all authors)
Kano, Yoshinobu, Jari Bjorne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, Kevin Cohen, Karin Verspoor, Christophe Roeder, Lawrence Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana Neves, Alberto Pascual-Montano, Arzucan Ozgur, Dragomir Radev, Sebastian Riedel, Rune Saetre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, and Jun’ichi Tsujii. 2011. “U-Compare Bio-Event Meta-Service : Compatible BioNLP Event Extraction Services.” BMC BIOINFORMATICS 12.
Vancouver
1.
Kano Y, Bjorne J, Ginter F, Salakoski T, Buyko E, Hahn U, et al. U-Compare bio-event meta-service : compatible BioNLP event extraction services. BMC BIOINFORMATICS. 2011;12.
IEEE
[1]
Y. Kano et al., “U-Compare bio-event meta-service : compatible BioNLP event extraction services,” BMC BIOINFORMATICS, vol. 12, 2011.
@article{2010323,
  abstract     = {Background: 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. 
Results: We have integrated nine event extraction systems in the U-Compare framework, making them inter-compatible and interoperable with other U-Compare components. The U-Compare event meta-service provides various meta-level features for comparison and ensemble of multiple event extraction systems. Experimental results show that the performance improvements achieved by the ensemble are significant. 
Conclusions: While individual event extraction systems themselves provide useful features for bio text mining, the U-Compare meta-service is expected to improve the accessibility to the individual systems, and to enable meta-level uses over multiple event extraction systems such as comparison and ensemble.},
  articleno    = {481},
  author       = {Kano, Yoshinobu and Bjorne, Jari and Ginter, Filip and Salakoski, Tapio and Buyko, Ekaterina and Hahn, Udo and Cohen, Kevin and Verspoor, Karin and Roeder, Christophe and Hunter, Lawrence and Kilicoglu, Halil and Bergler, Sabine and Van Landeghem, Sofie and Van Parys, Thomas and Van de Peer, Yves and Miwa, Makoto and Ananiadou, Sophia and Neves, Mariana and Pascual-Montano, Alberto and Ozgur, Arzucan and Radev, Dragomir and Riedel, Sebastian and Saetre, Rune and Chun, Hong-Woo and Kim, Jin-Dong and Pyysalo, Sampo and Ohta, Tomoko and Tsujii, Jun'ichi},
  issn         = {1471-2105},
  journal      = {BMC BIOINFORMATICS},
  keywords     = {INFORMATION EXTRACTION,text-mining,BioNLP,event extraction,meta-service,CORPUS},
  language     = {eng},
  pages        = {9},
  title        = {U-Compare bio-event meta-service : compatible BioNLP event extraction services},
  url          = {http://dx.doi.org/10.1186/1471-2105-12-481},
  volume       = {12},
  year         = {2011},
}

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