title: BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.
abstract: BioC is a simple XML format for text, annotations and relations, and was developed to achieve interoperability for biomedical text processing. Following the success of BioC in BioCreative IV, the BioCreative V BioC track addressed a collaborative task to build an assistant system for BioGRID curation. In this paper, we describe the framework of the collaborative BioC task and discuss our findings based on the user survey. This track consisted of eight subtasks including gene/protein/organism named entity recognition, protein-protein/genetic interaction passage identification and annotation visualization. Using BioC as their data-sharing and communication medium, nine teams, world-wide, participated and contributed either new methods or improvements of existing tools to address different subtasks of the BioC track. Results from different teams were shared in BioC and made available to other teams as they addressed different subtasks of the track. In the end, all submitted runs were merged using a machine learning classifier to produce an optimized output. The biocurator assistant system was evaluated by four BioGRID curators in terms of practical usability. The curators' feedback was overall positive and highlighted the user-friendly design and the convenient gene/protein curation tool based on text mining.Database URL: http://www.biocreative.org/tasks/biocreative-v/track-1-bioc/.
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors: Sun
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authors: Kim
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors: Rezarta
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authors: Islamaj Doğan
authors: Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada.
authors: Andrew
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authors: Chatr-Aryamontri
authors: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
authors: Christie S
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authors: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
authors: Rose
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authors: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
authors: Jennifer
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authors: Rust
authors: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK.
authors: Riza
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authors: Batista-Navarro
authors: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK.
authors: Jacob
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authors: Carter
authors: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK.
authors: Sophia
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authors: Ananiadou
authors: DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
authors: Sérgio
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authors: DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
authors: André
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authors: BMD Software, Lda, Rua Calouste Gulbenkian 1, 3810-074 Aveiro, Portugal.
authors: David
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authors: Campos
authors: DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
authors: José Luís
authors: JL
authors: Oliveira
authors: Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
authors: Onkar
authors: O
authors: Singh
authors: School of Public Health and Community Medicine, University of New South Wales, Kensington NSW 2033, Australia Prince of Wales Clinical School, University of New South Wales, Kensington NSW 2033, Australia.
authors: Jitendra
authors: J
authors: Jonnagaddala
authors: Department of Computer Science and Information Engineering, National Taitung University, Taitung, Taiwan.
authors: Hong-Jie
authors: HJ
authors: Dai
authors: Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
authors: Emily Chia-Yu
authors: EC
authors: Su
authors: Institute of Information Science, Academia Sinica, Taipei, Taiwan Department of Information Management, National Taiwan University, Taipei, Taiwan.
authors: Yung-Chun
authors: YC
authors: Chang
authors: Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan.
authors: Yu-Chen
authors: YC
authors: Su
authors: Institute of Information Science, Academia Sinica, Taipei, Taiwan.
authors: Chun-Han
authors: CH
authors: Chu
authors: Department of Information Management, National Taiwan University, Taipei, Taiwan.
authors: Chien Chin
authors: CC
authors: Chen
authors: Institute of Information Science, Academia Sinica, Taipei, Taiwan.
authors: Wen-Lian
authors: WL
authors: Hsu
authors: Computer & Information Sciences, University of Delaware, Newark, DE 19716, USA.
authors: Yifan
authors: Y
authors: Peng
authors: Computer & Information Sciences, University of Delaware, Newark, DE 19716, USA Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19716, USA.
authors: Cecilia
authors: C
authors: Arighi
authors: Computer & Information Sciences, University of Delaware, Newark, DE 19716, USA Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19716, USA.
authors: Cathy H
authors: CH
authors: Wu
authors: Computer & Information Sciences, University of Delaware, Newark, DE 19716, USA.
authors: K
authors: K
authors: Vijay-Shanker
authors: Department of Computer Engineering, Boğaziçi University, Bebek, 34342 Istanbul, Turkey.
authors: Ferhat
authors: F
authors: Aydın
authors: Department of Computer Engineering, Boğaziçi University, Bebek, 34342 Istanbul, Turkey.
authors: Zehra Melce
authors: ZM
authors: Hüsünbeyi
authors: Department of Computer Engineering, Boğaziçi University, Bebek, 34342 Istanbul, Turkey.
authors: Arzucan
authors: A
authors: Özgür
authors: Department of Biomedical Informatics, Asan Medical Center, 138-736 Seoul, South Korea.
authors: Soo-Yong
authors: SY
authors: Shin
authors: Department of Computer Engineering, Myongji University, 449-728 Yongin, South Korea.
authors: Dongseop
authors: D
authors: Kwon
authors: Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
authors: Kara
authors: K
authors: Dolinski
authors: Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
authors: Mike
authors: M
authors: Tyers
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
authors: W John
authors: WJ
authors: Wilbur
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA comeau@ncbi.nlm.nih.gov.
authors: Donald C
authors: DC
authors: Comeau
mesh_terms: D066289:Data Curation / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D001330:Electronic Data Processing / Q000379:methods*; D033181:Information Dissemination / Q000379:methods*