GLYCOBROWSER: A TOOL FOR CONTEXTUAL VISUALIZATION OF BIOL DATA & PATHWAYS

GLYCOBROWSER：生物数据上下文可视化工具

• 批准号: 8363023
• 负责人: WILLIAM YORK
• 金额: $ 3.96万
• 依托单位: UNIVERSITY OF GEORGIA
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-06-01 至 2012-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8363023
• 关键词: Address; Data; Funding; Genes; Grant; Imagery; Knowledge; Link; Metabolic Pathway; Methods; National Center for Research Resources; Ontology; Pathway interactions; Polysaccharides; Principal Investigator; Proteomics; Research; Research Infrastructure; Resources; Source; Structure; Technology; The Sun; Transcript; Transferase; United States National Institutes of Health; cost; flexibility; graphical user interface; tool; transcriptomics

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Glycoscientists can only make efficient use of the formalized knowledge embedded in our ontologies if they are provided with flexible interfaces that allow them to visualize this knowledge in a format that makes intuitive sense. The ontology itself consists of nodes and edges, whose meanings may not be obvious to the glycoscientist. To be useful, this information must be presented in a more familiar format. We addressed this need by developing GlycoBrowser, a tool for the visualization of ontological information in the glycomics domain. GlycoBrowser leverages the capabilities of GlycoVault, along with several other technologies, including RDF (http://www.w3.org/RDF/), AJAX (http://developers.sun.com/ajax/), Javascript, BRAHMS, etc. to represent structural information in a way that is intuitive for glycobiologists and to link this information to experimental data (glycomics, proteomics, and transcriptomics analyses). GycoBrowser provides a graphical display of glycan biosynthetic pathways and associated experimental data. Glycans are rendered "on the fly" using the standard representation endorsed by the Consortium for Functional Glycomics (CFG). GlycoBrowser include a powerful and flexible graphical interface, including methods for building glycan structures from canonical components that are represented in the GlycO ontology. For example, GlycoBrowser supports rendering of a larger segment of the metabolic pathway and relevant experimental data (such as the abundances of the various glycans and the transcript levels for various glycosyl transferase-encoding genes) are shown below the pathway.

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 子项目的主要研究者可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 糖科学家只能有效地利用嵌入在我们的本体中的形式化知识，如果他们提供灵活的接口，使他们能够可视化这种知识的格式，使直观的感觉。 本体本身由节点和边组成，其含义可能对糖科学家来说并不明显。 为了有用，这些信息必须以更熟悉的格式呈现。 我们通过开发GlycoBrowser，一种用于在糖组学领域中可视化本体信息的工具来解决这一需求。 GlycoBrowser利用GlycoVault的功能，沿着其他几种技术，包括RDF（http：//www.w3.org/RDF/）、AJAX（http：//developers.sun.com/ajax/）、JavaScript、BRAHMS等，以糖生物学家直观的方式表示结构信息，并将此信息与实验数据（糖组学、蛋白质组学和转录组学分析）联系起来。 GycoBrowser提供聚糖生物合成途径和相关实验数据的图形显示。 使用功能糖组学协会（CFG）认可的标准表示法“即时”呈现聚糖。 GlycoBrowser包括一个强大而灵活的图形界面，包括从GlycO本体中表示的规范组件构建聚糖结构的方法。 例如，GlycoBrowser支持呈现代谢途径的较大部分，相关实验数据（如各种聚糖的丰度和各种糖基转移酶编码基因的转录水平）显示在途径下方。