title: The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011.
abstract: BACKGROUND
  The Genia task, when it was introduced in 2009, was the first community-wide effort to address a fine-grained, structural information extraction from biomedical literature. Arranged for the second time as one of the main tasks of BioNLP Shared Task 2011, it aimed to measure the progress of the community since 2009, and to evaluate generalization of the technology to full text papers. The Protein Coreference task was arranged as one of the supporting tasks, motivated from one of the lessons of the 2009 task that the abundance of coreference structures in natural language text hinders further improvement with the Genia task.
  
  
  RESULTS
  The Genia task received final submissions from 15 teams. The results show that the community has made a significant progress, marking 74% of the best F-score in extracting bio-molecular events of simple structure, e.g., gene expressions, and 45% ~ 48% in extracting those of complex structure, e.g., regulations. The Protein Coreference task received 6 final submissions. The results show that the coreference resolution performance in biomedical domain is lagging behind that in newswire domain, cf. 50% vs. 66% in MUC score. Particularly, in terms of protein coreference resolution the best system achieved 34% in F-score.
  
  
  CONCLUSIONS
  Detailed analysis performed on the results improves our insight into the problem and suggests the directions for further improvements.
authors: Database Center for Life Science, Research Organization of Information and Science, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, Japan. jdkim@dbcls.rois.ac.jp
authors: Jin-Dong
authors: JD
authors: Kim
authors: Ngan
authors: N
authors: Nguyen
authors: Yue
authors: Y
authors: Wang
authors: Jun'ichi
authors: J
authors: Tsujii
authors: Toshihisa
authors: T
authors: Takagi
authors: Akinori
authors: A
authors: Yonezawa
mesh_terms: D003226:Congresses as Topic; D015870:Gene Expression; D007256:Information Systems; D009323:Natural Language Processing; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D011506:Proteins