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: 9391499
• 负责人: Raja Mazumder
• 金额: $ 200万
• 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 2022-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9391499
• 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; Imagery; Intuition; Knowledge; Knowledge Discovery; Link; Lipids; Literature; Manuals; Metadata; Molecular; Mutation; Names; Ontology; Pathology; Pathway interactions; Polysaccharides; Property; Proteomics; Protocols documentation; Reaction; Research; Research Infrastructure; Resource Informatics; Resources; Retrieval; Role; Scientist; Seeds; Source; Source Code; Structure; System; Training; Visualization software; base; data acquisition; data integration; data mining; data sharing; 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 尽管持续不断的技术进步正在加快数据采集的速度和复杂性， 糖科学，将这些数据转化为糖生物学知识、洞察和理解是 由于促进它们与生物学知识整合的工具数量有限，速度缓慢 遗传学、蛋白质组学、病理学和其他学科。我们的拨款申请描述了发展 集成的、可扩展的、跨学科的资源，提供工具和数据来解决特定问题 目前只能通过广泛的基于文献的研究和 从不同的数据库和网站手动收集数据。利用我们在以下方面获得的见解 规划赠款活动，包括以评估现有资源和社区为重点的讲习班 根据需要，我们建议开发广泛相关和可持续的糖信息学资源，以连接 随着数据的爆炸性增长，糖科学正在给生物学带来革命性的变化。我们发现了关键的差距， 需要填补和克服必须克服的挑战，以创造持久和可持续的 糖信息学资源，超越了将糖链数据映射到基因和蛋白质以识别和 整合EMBL-EBI、NCBI、UniProt、UniCarbKB、CAZy、gene等不同的多学科知识 本体论和其他来源。为了最大化这些资源之间的协同作用，我们提出了一种新的多糖 阵列数据存储库和增强的本体，以促进多糖和糖共轭化合物的集成 表达和与其他信息的交互数据。在以下背景下评估这些数据 关于基因突变、基因表达、蛋白质功能和其他现象的知识将提供 在系统水平上理解糖基化在疾病和疾病中的作用的新机会 发展。这一全面的数据集成框架将为 涉及与糖生物学相关的不同数据类型的复杂查询。所需的技术进步 实现该框架包括数据证据标记、本体和标准开发，以及 支持数据挖掘、共享和传播的新界面。社区参与，尤其是 与不擅长糖生物学的科学家合作，将强调最大限度地提高 我们的资源。我们将开发一个门户网站，以标准格式公开所有这些信息 在NCBI和EMBL-EBI的支持下，我们开发了新的格式，促进了数据及其 最终集成到这些广泛使用的信息学资源中。