BioC interoperability track overview

Donald C Comeau; Riza Theresa Batista-Navarro; Hong-Jie Dai; Rezarta Islamaj Doğan; Antonio Jimeno Yepes; Ritu Khare; Zhiyong Lu; Hernani Marques; Carolyn J Mattingly; Mariana Neves; Yifan Peng; Rafal Rak; Fabio Rinaldi; Richard Tzong-Han Tsai; Karin Verspoor; Thomas C Wiegers; Cathy H Wu; W John Wilbur

doi:10.1093/database/bau053

BioC interoperability track overview

Database (Oxford). 2014 Jun 30:2014:bau053. doi: 10.1093/database/bau053. Print 2014.

Authors

Donald C Comeau¹, Riza Theresa Batista-Navarro², Hong-Jie Dai², Rezarta Islamaj Doğan², Antonio Jimeno Yepes², Ritu Khare², Zhiyong Lu², Hernani Marques², Carolyn J Mattingly², Mariana Neves³, Yifan Peng², Rafal Rak², Fabio Rinaldi², Richard Tzong-Han Tsai², Karin Verspoor³, Thomas C Wiegers², Cathy H Wu³, W John Wilbur²

Affiliations

¹ National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA comeau@ncbi.nlm.nih.gov.
² National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
³ National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Universität zu Berlin, Berlin 10099, Germany, Berlin Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin 13353, Germany, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan, R.O.C., Health and Biomedical Informatics Centre, The University of Melbourne, Parkville, Victoria Australia 3010, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USANational Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA, National Centre for Text Mining and School of Computer Science, University of Manchester, Manchester M1 7DN, UK, Graduate Institute of BioMedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan, R.O.C., Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria Australia 3010, Institute of Computational Linguistics, University of Zurich, Zurich 8050, Switzerland, Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695-7617, USA, WBI, Institute for Computer Science, Humboldt-Univers

Abstract

BioC is a new simple XML format for sharing biomedical text and annotations and libraries to read and write that format. This promotes the development of interoperable tools for natural language processing (NLP) of biomedical text. The interoperability track at the BioCreative IV workshop featured contributions using or highlighting the BioC format. These contributions included additional implementations of BioC, many new corpora in the format, biomedical NLP tools consuming and producing the format and online services using the format. The ease of use, broad support and rapidly growing number of tools demonstrate the need for and value of the BioC format. Database URL: http://bioc.sourceforge.net/.

Published by Oxford University 2014. This work is written by US Government employees and is in the public domain in the US.

Publication types

Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Review

MeSH terms

Biomedical Research
Computational Biology*
Data Mining*
Database Management Systems
Databases, Factual
Internet
Natural Language Processing*
Software*

Abstract

Publication types

MeSH terms

Grants and funding