title: PIPE: a protein-protein interaction passage extraction module for BioCreative challenge.
abstract: Identifying the interactions between proteins mentioned in biomedical literatures is one of the frequently discussed topics of text mining in the life science field. In this article, we propose PIPE, an interaction pattern generation module used in the Collaborative Biocurator Assistant Task at BioCreative V (http://www.biocreative.org/) to capture frequent protein-protein interaction (PPI) patterns within text. We also present an interaction pattern tree (IPT) kernel method that integrates the PPI patterns with convolution tree kernel (CTK) to extract PPIs. Methods were evaluated on LLL, IEPA, HPRD50, AIMed and BioInfer corpora using cross-validation, cross-learning and cross-corpus evaluation. Empirical evaluations demonstrate that our method is effective and outperforms several well-known PPI extraction methods. DATABASE URL.
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei, Taiwan Department of Information Management, National Taiwan University, Taipei, Taiwan hsu@iis.sinica.edu.tw changyc@iis.sinica.edu.tw.
authors.forename: Yung-Chun
authors.initials: YC
authors.lastname: Chang
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei, Taiwan.
authors.forename: Chun-Han
authors.initials: CH
authors.lastname: Chu
authors.affiliation: Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan.
authors.forename: Yu-Chen
authors.initials: YC
authors.lastname: Su
authors.affiliation: Department of Information Management, National Taiwan University, Taipei, Taiwan.
authors.forename: Chien Chin
authors.initials: CC
authors.lastname: Chen
authors.affiliation: Institute of Information Science, Academia Sinica, Taipei, Taiwan hsu@iis.sinica.edu.tw.
authors.forename: Wen-Lian
authors.initials: WL
authors.lastname: Hsu
mesh_terms: D000818:Animals; D057225:Data Mining / Q000379:methods*; D006801:Humans; D011506:Proteins / Q000235:genetics* / Q000378:metabolism*
chemical_list: D011506:Proteins