title: BelSmile: a biomedical semantic role labeling approach for extracting biological expression language from text.
abstract: Biological expression language (BEL) is one of the most popular languages to represent the causal and correlative relationships among biological events. Automatically extracting and representing biomedical events using BEL can help biologists quickly survey and understand relevant literature. Recently, many researchers have shown interest in biomedical event extraction. However, the task is still a challenge for current systems because of the complexity of integrating different information extraction tasks such as named entity recognition (NER), named entity normalization (NEN) and relation extraction into a single system. In this study, we introduce our BelSmile system, which uses a semantic-role-labeling (SRL)-based approach to extract the NEs and events for BEL statements. BelSmile combines our previous NER, NEN and SRL systems. We evaluate BelSmile using the BioCreative V BEL task dataset. Our system achieved an F-score of 27.8%, ∼7% higher than the top BioCreative V system. The three main contributions of this study are (i) an effective pipeline approach to extract BEL statements, and (ii) a syntactic-based labeler to extract subject-verb-object tuples. We also implement a web-based version of BelSmile (iii) that is publicly available at iisrserv.csie.ncu.edu.tw/belsmile.
authors.affiliation: Department of Computer Science, National Tsing-Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu, Taiwan 30013, Republic of China.
authors.forename: Po-Ting
authors.initials: PT
authors.lastname: Lai
authors.affiliation: Department of Computer Science and Information Engineering, National Central University, No. 300, Zhongda Road, Zhongli, Taoyuan, Taiwan 320, Republic of China and.
authors.forename: Yu-Yan
authors.initials: YY
authors.lastname: Lo
authors.affiliation: Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, No.1, Section 1, Renai Road, Taipei, Taiwan 10002, Republic of China.
authors.forename: Ming-Siang
authors.initials: MS
authors.lastname: Huang
authors.affiliation: Department of Computer Science and Information Engineering, National Central University, No. 300, Zhongda Road, Zhongli, Taoyuan, Taiwan 320, Republic of China and.
authors.forename: Yu-Cheng
authors.initials: YC
authors.lastname: Hsiao
authors.affiliation: Department of Computer Science and Information Engineering, National Central University, No. 300, Zhongda Road, Zhongli, Taoyuan, Taiwan 320, Republic of China and thtsai@csie.ncu.edu.tw.
authors.forename: Richard Tzong-Han
authors.initials: RT
authors.lastname: Tsai
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D006801:Humans; D009323:Natural Language Processing; D012660:Semantics; D012984:Software