title: Evaluating contributions of natural language parsers to protein-protein interaction extraction.
abstract: BACKGROUND
  While text mining technologies for biomedical research have gained popularity as a way to take advantage of the explosive growth of information in text form in biomedical papers, selecting appropriate natural language processing (NLP) tools is still difficult for researchers who are not familiar with recent advances in NLP. This article provides a comparative evaluation of several state-of-the-art natural language parsers, focusing on the task of extracting protein-protein interaction (PPI) from biomedical papers. We measure how each parser, and its output representation, contributes to accuracy improvement when the parser is used as a component in a PPI system.
  
  
  RESULTS
  All the parsers attained improvements in accuracy of PPI extraction. The levels of accuracy obtained with these different parsers vary slightly, while differences in parsing speed are larger. The best accuracy in this work was obtained when we combined Miyao and Tsujii's Enju parser and Charniak and Johnson's reranking parser, and the accuracy is better than the state-of-the-art results on the same data.
  
  
  BACKGROUND
  The PPI extraction system used in this work (AkanePPI) is available online at http://www-tsujii.is.s.u-tokyo.ac.jp/downloads/downloads.cgi. The evaluated parsers are also available online from each developer's site.
authors.affiliation: Department of Computer Science, University of Tokyo, Tokyo, Japan. yusuke@is.s.u-tokyo.ac.jp
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Miyao
authors.forename: Kenji
authors.initials: K
authors.lastname: Sagae
authors.forename: Rune
authors.initials: R
authors.lastname: Saetre
authors.forename: Takuya
authors.initials: T
authors.lastname: Matsuzaki
authors.forename: Jun'ichi
authors.initials: J
authors.lastname: Tsujii
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D009323:Natural Language Processing; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D011506:Proteins