title: BioCreative V CDR task corpus: a resource for chemical disease relation extraction.
abstract: Community-run, formal evaluations and manually annotated text corpora are critically important for advancing biomedical text-mining research. Recently in BioCreative V, a new challenge was organized for the tasks of disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction. Given the nature of both tasks, a test collection is required to contain both disease/chemical annotations and relation annotations in the same set of articles. Despite previous efforts in biomedical corpus construction, none was found to be sufficient for the task. Thus, we developed our own corpus called BC5CDR during the challenge by inviting a team of Medical Subject Headings (MeSH) indexers for disease/chemical entity annotation and Comparative Toxicogenomics Database (CTD) curators for CID relation annotation. To ensure high annotation quality and productivity, detailed annotation guidelines and automatic annotation tools were provided. The resulting BC5CDR corpus consists of 1500 PubMed articles with 4409 annotated chemicals, 5818 diseases and 3116 chemical-disease interactions. Each entity annotation includes both the mention text spans and normalized concept identifiers, using MeSH as the controlled vocabulary. To ensure accuracy, the entities were first captured independently by two annotators followed by a consensus annotation: The average inter-annotator agreement (IAA) scores were 87.49% and 96.05% for the disease and chemicals, respectively, in the test set according to the Jaccard similarity coefficient. Our corpus was successfully used for the BioCreative V challenge tasks and should serve as a valuable resource for the text-mining research community.Database URL: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/.
authors.affiliation: 1Institute of Medical Information, Chinese Academy of Medical Sciences, Beijing 100020, China.
authors.forename: Jiao
authors.initials: J
authors.lastname: Li
authors.affiliation: 1Institute of Medical Information, Chinese Academy of Medical Sciences, Beijing 100020, China.
authors.forename: Yueping
authors.initials: Y
authors.lastname: Sun
authors.affiliation: 2Department of Biological Sciences and the Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA.
authors.forename: Robin J
authors.initials: RJ
authors.lastname: Johnson
authors.affiliation: 2Department of Biological Sciences and the Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA.
authors.forename: Daniela
authors.initials: D
authors.lastname: Sciaky
authors.affiliation: 3National Center for Biotechnology Information, Bethesda, MD 20894, USA.
authors.forename: Chih-Hsuan
authors.initials: CH
authors.lastname: Wei
authors.affiliation: 3National Center for Biotechnology Information, Bethesda, MD 20894, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Leaman
authors.affiliation: 2Department of Biological Sciences and the Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA.
authors.forename: Allan Peter
authors.initials: AP
authors.lastname: Davis
authors.affiliation: 2Department of Biological Sciences and the Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA.
authors.forename: Carolyn J
authors.initials: CJ
authors.lastname: Mattingly
authors.affiliation: 2Department of Biological Sciences and the Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA.
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Wiegers
authors.affiliation: 3National Center for Biotechnology Information, Bethesda, MD 20894, USA zhiyong.lu@nih.gov.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Lu
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual; D004194:Disease; D006801:Humans; D043922:Toxicogenetics / Q000379:methods*