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Database (Oxford). 2016 Sep 1;2016. pii: baw121. doi: 10.1093/database/baw121. Print 2016.

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.

Author information

1
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
2
Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada.
3
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
4
National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, UK.
5
DETI/IEETA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
6
BMD Software, Lda, Rua Calouste Gulbenkian 1, 3810-074 Aveiro, Portugal.
7
Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
8
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.
9
Department of Computer Science and Information Engineering, National Taitung University, Taitung, Taiwan.
10
Institute of Information Science, Academia Sinica, Taipei, Taiwan Department of Information Management, National Taiwan University, Taipei, Taiwan.
11
Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan.
12
Institute of Information Science, Academia Sinica, Taipei, Taiwan.
13
Department of Information Management, National Taiwan University, Taipei, Taiwan.
14
Computer & Information Sciences, University of Delaware, Newark, DE 19716, USA.
15
Computer & Information Sciences, University of Delaware, Newark, DE 19716, USA Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE 19716, USA.
16
Department of Computer Engineering, Boğaziçi University, Bebek, 34342 Istanbul, Turkey.
17
Department of Biomedical Informatics, Asan Medical Center, 138-736 Seoul, South Korea.
18
Department of Computer Engineering, Myongji University, 449-728 Yongin, South Korea.
19
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.
20
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA comeau@ncbi.nlm.nih.gov.

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/.

PMID:
27589962
PMCID:
PMC5009341
DOI:
10.1093/database/baw121
[Indexed for MEDLINE]
Free PMC Article

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