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生物信息学互操作性赛道概述。

BioC interoperability track overview.

作者信息

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

机构信息

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

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.

出版信息

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

DOI:10.1093/database/bau053
PMID:24980129
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4074764/
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/.

摘要

BioC是一种用于共享生物医学文本、注释及读写该格式库的新型简单XML格式。这推动了用于生物医学文本自然语言处理(NLP)的可互操作工具的开发。BioCreative IV研讨会的互操作性专题展示了使用或突出BioC格式的成果。这些成果包括BioC的更多实现、该格式的许多新语料库、使用和生成该格式的生物医学NLP工具以及使用该格式的在线服务。其易用性、广泛支持和迅速增长的工具数量证明了BioC格式的必要性和价值。数据库网址:http://bioc.sourceforge.net/ 。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2215/4074764/79e6c3a8f6e0/bau053f3p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2215/4074764/2bde7c67b83c/bau053f1p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2215/4074764/91c046574070/bau053f2p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2215/4074764/79e6c3a8f6e0/bau053f3p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2215/4074764/2bde7c67b83c/bau053f1p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2215/4074764/91c046574070/bau053f2p.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2215/4074764/79e6c3a8f6e0/bau053f3p.jpg

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2
BioC implementations in Go, Perl, Python and Ruby.用Go、Perl、Python和Ruby实现的BioC。
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3
Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus.用于注释BioC文集的自然语言处理管道及其在NCBI疾病语料库中的应用。
Database (Oxford). 2019 Jan 1;2019:bay147. doi: 10.1093/database/bay147.
4
The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions.BioC-BioGRID语料库:为蛋白质-蛋白质和基因相互作用的编目而注释的全文文章。
Database (Oxford). 2017 Jan 10;2017. doi: 10.1093/database/baw147. Print 2017.
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Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.生物编目及其他领域对生物医学文本挖掘的迫切需求:机遇与挑战。
Database (Oxford). 2016 Dec 26;2016. doi: 10.1093/database/baw161. Print 2016.
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PubMedPortable: A Framework for Supporting the Development of Text Mining Applications.PubMed便携式:支持文本挖掘应用开发的框架。
PLoS One. 2016 Oct 5;11(10):e0163794. doi: 10.1371/journal.pone.0163794. eCollection 2016.
7
BioC viewer: a web-based tool for displaying and merging annotations in BioC.BioC查看器:一种用于在BioC中显示和合并注释的基于网络的工具。
Database (Oxford). 2016 Aug 10;2016. doi: 10.1093/database/baw106. Print 2016.
8
NTTMUNSW BioC modules for recognizing and normalizing species and gene/protein mentions.用于识别和规范化物种以及基因/蛋白质提及的新南威尔士大学(UNSW)生物信息学模块。
Database (Oxford). 2016 Jul 27;2016. doi: 10.1093/database/baw111. Print 2016.
9
Beyond accuracy: creating interoperable and scalable text-mining web services.超越准确性:创建可互操作且可扩展的文本挖掘网络服务。
Bioinformatics. 2016 Jun 15;32(12):1907-10. doi: 10.1093/bioinformatics/btv760. Epub 2016 Feb 16.
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