Customizable views on semantically integrated networks for systems biology.
Customizable views on semantically integrated networks for systems biology.
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DOI：
10.1093/bioinformatics/btr134
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发表时间：
2011-05-01
期刊：
影响因子：
--
通讯作者：
Wipat A
中科院分区：
文献类型：
--
作者：
Weile J;Pocock M;Cockell SJ;Lord P;Dewar JM;Holstein EM;Wilkinson D;Lydall D;Hallinan J;Wipat A
动机：后基因组时代高通量技术的兴起导致了大量生物数据的产生。其中许多数据集都可以在互联网上免费获得。充分利用这些数据对生物信息学家来说是一个重大挑战。为了应对这一挑战，人们提出了各种整合数据的策略。最有前途的方法之一是开发语义丰富的集成数据集。尽管非常适合计算操作，但此类集成数据集通常太大且复杂，无法轻松可视化和交互式探索。结果：我们使用语义数据集成工具 Ondex 创建了酿酒酵母的集成数据集，并开发了一种基于视图的可视化技术，可以对集成数据进行简洁的图形表示。该技术是在 Cytoscape 的一个名为 OndexView 的插件中实现的。我们使用 OndexView 研究酿酒酵母的端粒维持情况。可用性：Ondex 酵母数据集和 Cytoscape 的 OndexView 插件可通过 http://bsu.ncl.ac.uk/ondexview 访问。联系方式：anil.wipat@ncl.ac.uk 补充信息：补充数据可在生物信息学在线获取。
Motivation: The rise of high-throughput technologies in the post-genomic era has led to the production of large amounts of biological data. Many of these datasets are freely available on the Internet. Making optimal use of these data is a significant challenge for bioinformaticians. Various strategies for integrating data have been proposed to address this challenge. One of the most promising approaches is the development of semantically rich integrated datasets. Although well suited to computational manipulation, such integrated datasets are typically too large and complex for easy visualization and interactive exploration. Results: We have created an integrated dataset for Saccharomyces cerevisiae using the semantic data integration tool Ondex, and have developed a view-based visualization technique that allows for concise graphical representations of the integrated data. The technique was implemented in a plug-in for Cytoscape, called OndexView. We used OndexView to investigate telomere maintenance in S. cerevisiae. Availability: The Ondex yeast dataset and the OndexView plug-in for Cytoscape are accessible at http://bsu.ncl.ac.uk/ondexview. Contact: anil.wipat@ncl.ac.uk Supplementary information: Supplementary data is available at Bioinformatics online.
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