title: CD-REST: a system for extracting chemical-induced disease relation in literature.
abstract: Mining chemical-induced disease relations embedded in the vast biomedical literature could facilitate a wide range of computational biomedical applications, such as pharmacovigilance. The BioCreative V organized a Chemical Disease Relation (CDR) Track regarding chemical-induced disease relation extraction from biomedical literature in 2015. We participated in all subtasks of this challenge. In this article, we present our participation system Chemical Disease Relation Extraction SysTem (CD-REST), an end-to-end system for extracting chemical-induced disease relations in biomedical literature. CD-REST consists of two main components: (1) a chemical and disease named entity recognition and normalization module, which employs the Conditional Random Fields algorithm for entity recognition and a Vector Space Model-based approach for normalization; and (2) a relation extraction module that classifies both sentence-level and document-level candidate drug-disease pairs by support vector machines. Our system achieved the best performance on the chemical-induced disease relation extraction subtask in the BioCreative V CDR Track, demonstrating the effectiveness of our proposed machine learning-based approaches for automatic extraction of chemical-induced disease relations in biomedical literature. The CD-REST system provides web services using HTTP POST request. The web services can be accessed fromhttp://clinicalnlptool.com/cdr The online CD-REST demonstration system is available athttp://clinicalnlptool.com/cdr/cdr.html. Database URL:http://clinicalnlptool.com/cdr;http://clinicalnlptool.com/cdr/cdr.html.
authors.affiliation: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Xu
authors.affiliation: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Yonghui
authors.initials: Y
authors.lastname: Wu
authors.affiliation: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Yaoyun
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Jingqi
authors.initials: J
authors.lastname: Wang
authors.affiliation: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
authors.forename: Hee-Jin
authors.initials: HJ
authors.lastname: Lee
authors.affiliation: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA hua.xu@uth.tmc.edu.
authors.forename: Hua
authors.initials: H
authors.lastname: Xu
mesh_terms: D057225:Data Mining; D019992:Databases as Topic; D004194:Disease; D006801:Humans; D012015:Reference Standards