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U-Compare Bio-Event Meta-Service: Compatible BioNLP Event Extraction Services

Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, Kevin Cohen, Katrin Verspoor, Christophe Roeder, Lawrence Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, U-Compare Bio-Event Meta-Service: Compatible BioNLP Event Extraction Services. BMC Bioinformatics 12(1), 481, 2011.



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.

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.

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.

BibTeX entry:

  title = {U-Compare Bio-Event Meta-Service: Compatible BioNLP Event Extraction Services},
  author = {Kano, Yoshinobu and Björne, Jari and Ginter, Filip and Salakoski, Tapio and Buyko, Ekaterina and Hahn, Udo and Cohen, Kevin and Verspoor, Katrin and Roeder, Christophe and Hunter, Lawrence and Kilicoglu, Halil and Bergler, Sabine and Van Landeghem, Sofie},
  journal = {BMC Bioinformatics},
  volume = {12},
  number = {1},
  publisher = {BioMed Central},
  pages = {481},
  year = {2011},

Belongs to TUCS Research Unit(s): Turku BioNLP Group

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