title: The CHEMDNER corpus of chemicals and drugs and its annotation principles.
abstract: The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability of a large, manually annotated text corpus is desirable. Furthermore, large corpora permit the robust evaluation and comparison of different approaches that detect chemicals in documents. We present the CHEMDNER corpus, a collection of 10,000 PubMed abstracts that contain a total of 84,355 chemical entity mentions labeled manually by expert chemistry literature curators, following annotation guidelines specifically defined for this task. The abstracts of the CHEMDNER corpus were selected to be representative for all major chemical disciplines. Each of the chemical entity mentions was manually labeled according to its structure-associated chemical entity mention (SACEM) class: abbreviation, family, formula, identifier, multiple, systematic and trivial. The difficulty and consistency of tagging chemicals in text was measured using an agreement study between annotators, obtaining a percentage agreement of 91. For a subset of the CHEMDNER corpus (the test set of 3,000 abstracts) we provide not only the Gold Standard manual annotations, but also mentions automatically detected by the 26 teams that participated in the BioCreative IV CHEMDNER chemical mention recognition task. In addition, we release the CHEMDNER silver standard corpus of automatically extracted mentions from 17,000 randomly selected PubMed abstracts. A version of the CHEMDNER corpus in the BioC format has been generated as well. We propose a standard for required minimum information about entity annotations for the construction of domain specific corpora on chemical and drug entities. The CHEMDNER corpus and annotation guidelines are available at: http://www.biocreative.org/resources/biocreative-iv/chemdner-corpus/.
authors: Structural Computational Biology Group, Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre, Madrid, Spain.
authors: Martin
authors: M
authors: Krallinger
authors: Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.
authors: Obdulia
authors: O
authors: Rabal
authors: Computational Intelligence Group, Department of Artificial Intelligence, Universidad Politecnica de Madrid, Madrid, Spain.
authors: Florian
authors: F
authors: Leitner
authors: Structural Computational Biology Group, Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre, Madrid, Spain.
authors: Miguel
authors: M
authors: Vazquez
authors: Faculte de Medecine La Timone, Marseille, Marseille, France.
authors: David
authors: D
authors: Salgado
authors: National Center for Biotechnology Information (NCBI), National Institutes of Health, Bethesda, USA.
authors: Zhiyong
authors: Z
authors: Lu
authors: National Center for Biotechnology Information (NCBI), National Institutes of Health, Bethesda, USA.
authors: Robert
authors: R
authors: Leaman
authors: Natural Language Processing Lab, Wuhan University, Wuhan, Hubei, PR China.
authors: Yanan
authors: Y
authors: Lu
authors: Natural Language Processing Lab, Wuhan University, Wuhan, Hubei, PR China.
authors: Donghong
authors: D
authors: Ji
authors: NextMove Software Ltd, Innovation Centre, Unit 23, Science Park, Milton Road, Cambridge, UK.
authors: Daniel M
authors: DM
authors: Lowe
authors: NextMove Software Ltd, Innovation Centre, Unit 23, Science Park, Milton Road, Cambridge, UK.
authors: Roger A
authors: RA
authors: Sayle
authors: National Centre for Text Mining, Manchester Institute of Biotechnology, Manchester, UK.
authors: Riza Theresa
authors: RT
authors: Batista-Navarro
authors: National Centre for Text Mining, Manchester Institute of Biotechnology, Manchester, UK.
authors: Rafal
authors: R
authors: Rak
authors: Humboldt-Universität zu Berlin, Knowledge Management in Bioinformatics, Berlin, Germany.
authors: Torsten
authors: T
authors: Huber
authors: Department of Computer Science, University College London, London, UK.
authors: Tim
authors: T
authors: Rocktäschel
authors: IEETA/DETI, University of Aveiro, Campus Universitario de Santiago, Aveiro, Portugal.
authors: Sérgio
authors: S
authors: Matos
authors: IEETA/DETI, University of Aveiro, Campus Universitario de Santiago, Aveiro, Portugal.
authors: David
authors: D
authors: Campos
authors: Department of Computer Science, Harbin Institute of Technology, Shenzhen Graduate School Shenzhen, GuangDong, PR China.
authors: Buzhou
authors: B
authors: Tang
authors: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, USA.
authors: Hua
authors: H
authors: Xu
authors: Database/Bioinformatics Laboratory, School of Electrical and Computer Engineering, Chungbuk National University, Cheongju, South Korea.
authors: Tsendsuren
authors: T
authors: Munkhdalai
authors: Database/Bioinformatics Laboratory, School of Electrical and Computer Engineering, Chungbuk National University, Cheongju, South Korea.
authors: Keun Ho
authors: KH
authors: Ryu
authors: RelAgent Pvt Ltd, IIT Madras Research Park, Taramani, Chennai, India.
authors: S V
authors: SV
authors: Ramanan
authors: RelAgent Pvt Ltd, IIT Madras Research Park, Taramani, Chennai, India.
authors: Senthil
authors: S
authors: Nathan
authors: Faculty of computer and information science, University of Ljubljana, Ljubljana, Slovenia.
authors: Slavko
authors: S
authors: Žitnik
authors: Faculty of computer and information science, University of Ljubljana, Ljubljana, Slovenia.
authors: Marko
authors: M
authors: Bajec
authors: OntoChem GmbH, Halle, Germany.
authors: Lutz
authors: L
authors: Weber
authors: OntoChem GmbH, Halle, Germany.
authors: Matthias
authors: M
authors: Irmer
authors: Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands.
authors: Saber A
authors: SA
authors: Akhondi
authors: Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands.
authors: Jan A
authors: JA
authors: Kors
authors: Information Technology Supporting Center, Institute of Scientific and Technical Information of China, Beijing, PR China.
authors: Shuo
authors: S
authors: Xu
authors: School of Economics and Management, Beijing Forestry University, Beijing, PR China.
authors: Xin
authors: X
authors: An
authors: Department of Computer Science and Engineering Indian institute of Technology, Patna, Bihar, India.
authors: Utpal Kumar
authors: UK
authors: Sikdar
authors: Department of Computer Science and Engineering Indian institute of Technology, Patna, Bihar, India.
authors: Asif
authors: A
authors: Ekbal
authors: Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan.
authors: Masaharu
authors: M
authors: Yoshioka
authors: Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan.
authors: Thaer M
authors: TM
authors: Dieb
authors: Department of Computing and Information Systems, University of Melbourne, Melbourne, Australia.
authors: Miji
authors: M
authors: Choi
authors: Department of Computing and Information Systems, University of Melbourne, Melbourne, Australia ; National ICT Australia Victoria Research Laboratory, West Melbourne, Australia.
authors: Karin
authors: K
authors: Verspoor
authors: Computer Science and Engineering, The Pennsylvania State University, Pennsylvania, USA.
authors: Madian
authors: M
authors: Khabsa
authors: Computer Science and Engineering, The Pennsylvania State University, Pennsylvania, USA ; Information Sciences and Technology, The Pennsylvania State University, Pennsylvania, USA.
authors: C Lee
authors: CL
authors: Giles
authors: Department of Health Sciences Research, Mayo College of Medicine, Rochester, USA.
authors: Hongfang
authors: H
authors: Liu
authors: Department of Health Sciences Research, Mayo College of Medicine, Rochester, USA.
authors: Komandur Elayavilli
authors: KE
authors: Ravikumar
authors: LaSIGE, Department of Informatics, Faculty of Sciences, University of Lisbon, Lisbon, Portugal.
authors: Andre
authors: A
authors: Lamurias
authors: LaSIGE, Department of Informatics, Faculty of Sciences, University of Lisbon, Lisbon, Portugal.
authors: Francisco M
authors: FM
authors: Couto
authors: Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
authors: Hong-Jie
authors: HJ
authors: Dai
authors: Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan.
authors: Richard Tzong-Han
authors: RT
authors: Tsai
authors: Department of Computer Engineering, Middle East Technical University, Ankara, Turkey.
authors: Caglar
authors: C
authors: Ata
authors: Department of Computer Engineering, Middle East Technical University, Ankara, Turkey.
authors: Tolga
authors: T
authors: Can
authors: Departament Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain ; Departament d'Informatica i Enginyeria Industrial, Univesitat de Lleida, Lleida, Spain.
authors: Anabel
authors: A
authors: Usié
authors: Departament Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain.
authors: Rui
authors: R
authors: Alves
authors: Computer Science Department, Universidad Carlos III de Madrid, Madrid, Spain.
authors: Isabel
authors: I
authors: Segura-Bedmar
authors: Computer Science Department, Universidad Carlos III de Madrid, Madrid, Spain.
authors: Paloma
authors: P
authors: Martínez
authors: Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.
authors: Julen
authors: J
authors: Oyarzabal
authors: Structural Computational Biology Group, Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre, Madrid, Spain.
authors: Alfonso
authors: A
authors: Valencia
keywords: BioCreative; ChemNLP; chemical entity recognition; chemical indexing; machine learning; named entity recognition; text mining