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

Yoshinobu Kano, Jari Bjorne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, Kevin Cohen, Karin Verspoor, Christophe Roeder, Lawrence Hunter, et al. (2011) BMC BIOINFORMATICS. 12.
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
INFORMATION EXTRACTION, text-mining, BioNLP, event extraction, meta-service, CORPUS
journal title
BMC BIOINFORMATICS
BMC Bioinformatics
volume
12
article number
481
pages
9 pages
Web of Science type
Article
Web of Science id
000301382700001
JCR category
MATHEMATICAL & COMPUTATIONAL BIOLOGY
JCR impact factor
2.751 (2011)
JCR rank
6/46 (2011)
JCR quartile
1 (2011)
ISSN
1471-2105
DOI
10.1186/1471-2105-12-481
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
2010323
handle
http://hdl.handle.net/1854/LU-2010323
date created
2012-01-31 20:25:32
date last changed
2016-12-21 15:41:31
@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},
  keyword      = {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},
}

Chicago
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.
APA
Kano, Y., Bjorne, J., Ginter, F., Salakoski, T., Buyko, E., Hahn, U., Cohen, K., et al. (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.
MLA
Kano, Yoshinobu , Jari Bjorne, Filip Ginter, et al. “U-Compare Bio-event Meta-service: Compatible BioNLP Event Extraction Services.” BMC BIOINFORMATICS 12 (2011): n. pag. Print.