Computational and Informatics Resources and Tools for Glycoscience Research

糖科学研究的计算和​​信息学资源和工具

• 批准号: 10178041
• 负责人: Raja Mazumder
• 金额: $ 194.24万
• 依托单位: UNIVERSITY OF GEORGIA
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2023-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10178041
• 关键词: Address; Anabolism; Applications Grants; Big Data; Binding; Biological; Biology; Biophysics; Carbohydrates; Code; Communities; Complex; Computer software; Coupled; DNA Sequence Alteration; Data; Data Analyses; Data Collection; Data Set; Databases; Development; Discipline; Disease; Documentation; Educational workshop; Enzymes; Explosion; Funding; Gene Expression; Gene Proteins; Genes; Genetic; Genomics; Glycobiology; Glycoconjugates; Grant; Guidelines; Infrastructure; Intuition; Knowledge; Knowledge Discovery; Link; Lipids; Literature; Manuals; Metadata; Molecular; Mutation; Names; Ontology; Pathology; Pathway interactions; Polysaccharides; Property; Proteomics; Protocols documentation; Reaction; Research; Resource Informatics; Resources; Retrieval; Role; Scientist; Seeds; Source; Source Code; Structure; System; Training; Visualization; Visualization software; base; community engagement; data acquisition; data integration; data mining; data repository; data sharing; diverse data; experience; glycosylation; hackathon; insight; multidisciplinary; protein function; repository; synergism; tool; web portal; web services; web site

PROJECT SUMMARY/ABSTRACT Although ongoing technical advances are accelerating the pace and sophistication of data acquisition in glycoscience, the transformation of these data to glycobiology knowledge, insight, and understanding is slowed by the limited number of tools that facilitate their integration with biological knowledge from genetics, proteomics, pathology, and other disciplines. Our grant application describes the development of an integrated, extendable, and cross-disciplinary resource providing tools and data to address specific scientific questions that can currently be answered only by extensive literature-based research and manual collection of data from disparate databases and websites. Using insight gained during our planning grant activities, including a workshop focused on evaluating existing resources and community needs, we propose to develop a broadly relevant and sustainable glycoinformatics resource to connect glycoscience with the explosion of data that is revolutionizing biology. We identified critical gaps that need to be filled and challenges that must be overcome to create an enduring and sustainable glycoinformatics resource that goes beyond mapping glycan data to genes and proteins to identify and integrate diverse multidisciplinary knowledge from EMBL-EBI, NCBI, UniProt, UniCarbKB, CAZy, Gene Ontology and other sources. To maximize synergy among these resources, we propose a new glycan array data repository and enhanced ontologies to facilitate integration of glycan and glycoconjugate expression and interaction data with other information. Evaluating these data in the context of knowledge about genetic mutations, gene expression, protein function and other phenomena will provide new opportunities for systems-level understanding of the roles of glycosylation in disease and development. This comprehensive data integration framework will provide unprecedented support for complex queries spanning diverse data types relevant to glycobiology. Technical advances required to implement this framework include evidence tagging of data, ontology and standards development, and new interfaces that enable data mining, sharing, and dissemination. Community engagement, especially with scientists who do not specialize in glycobiology, will be emphasized to maximize the relevance of our resource. We will develop a portal to make all this information publicly available in standard formats supported by NCBI and EMBL-EBI and in new formats we develop, promoting sharing of data and their ultimate integration into these widely used informatics resources.

项目摘要/摘要 尽管持续的技术进步正在加速数据获取的步伐和复杂性 糖科学，这些数据转换为糖生物学知识，洞察力和理解是 对有限数量的工具减慢了促进其与生物学知识的融合 遗传学，蛋白质组学，病理和其他学科。我们的赠款申请描述了开发 综合，可扩展和跨学科资源提供工具和数据，以解决特定 科学问题目前只能通过广泛的基于文献的研究来回答 手动从不同数据库和网站收集数据。使用在我们期间获得的见解 计划赠款活动，包括专注于评估现有资源和社区的研讨会 需求，我们建议开发一种广泛相关且可持续的糖节形式资源，以连接 与正在革命生物学的数据的爆炸爆炸一起爆炸。我们确定了关键差距 需要填补和必须克服的挑战才能创建一个持久和可持续的 糖化资源超出将聚糖数据映射到基因和蛋白质以识别和识别和 整合来自Embl-Ebi，NCBI，Uniprot，Unicarbkb，Cazy，Gene的多元学科知识 本体和其他来源。为了最大化这些资源之间的协同作用，我们提出了一个新的聚糖 阵列数据存储库和增强的本体，以促进聚糖和糖缀合物的整合 表达和交互数据与其他信息。在 关于遗传突变，基因表达，蛋白质功能和其他现象的知识将提供 系统级别理解糖基化在疾病中的作用的新机会 发展。这个全面的数据集成框架将为空前的支持提供 复杂的查询涵盖与糖生物学相关的多种数据类型。需要技术进步 实施此框架包括数据标签，本体论和标准开发以及 可以实现数据挖掘，共享和传播的新接口。特别是社区参与 对于不专门从事糖生物学的科学家，将强调最大化的相关性 我们的资源。我们将开发一个门户网站以使所有这些信息以标准格式公开提供 在NCBI和EMBL-EBI的支持下以及我们开发的新格式，促进数据及其共享 这些广泛使用的信息学资源中的最终集成。