The Protein Structure Inittiative Knowledgebase

蛋白质结构倡议知识库

• 批准号: 8101214
• 负责人: Helen M Berman
• 金额: $ 232.37万
• 依托单位: RUTGERS, THE STATE UNIV OF N.J.
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-07-01 至 2015-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8101214
• 关键词: Protein; Structure; Inittiative; Knowledgebase

DESCRIPTION (provided by applicant): Protein Structure Initiative (PSI) Knowledgebase. We propose to create an Information repository and web portal called the Structural Biology Knowledgebase (SBKB), which will be an enhanced version of the current Structural Genomics Knowledgebase (SGKB). The SBKB will integrate the products of the PSI:Biology centers with data from external databases and community input to provide comprehensive sequence, structural, and functional information about all protein sequences In the structural genomics target tracking database, TargetDB, and the protein structure repository, the Protein Data Bank. In addition, we will continue to collaborate with the Nature Publishing Group to provide a "Gateway" to all information about structural biology and genomics. The SGKB has organized the products of the PSI efforts into seven modules (Experimental Data Tracking, Technology, Materials, Modeling, Annotation, Publications, and Metrics) so that all biological and biomedical researchers can access this information from a central "one-stop shop". In this proposal, we describe our plan to enhance the existing modules, and propose a new format to organize the underlying SBKB data into four categorical views: the Targets, Methods, Structure-Sequence-Function, and Models Hubs. This approach improves upon the current single-interface method by providing users with focused views of the information. We are also in the process of developing a data visualization tool that allows users to dynamically explore relationships in the SBKB data to enable the creation of new hypotheses. The SBKB will play an important role in the coordination of activities across the PSI:Biology Network and in outreach to diverse biological fields. Existing systems will be used to coordinate internal communications for PSI:Biology Network participants. In order to increase community involvement, we describe an recent enhancement to the community-nominated targets system, and propose a new web tool that collects community annotations for structures and targets and enables collaborations. Our goal is for the SBKB to become an engaging and widely-used resource for all biological and biomedical communities. PUBLIC HEALTH RELEVANCE: The Structural Biology Knowledgebase will facilitate and simplify access to protein sequence, structure, and functional information for users from a variety of biological disciplines. In this way, it will be possible to gain both a broad and deep understanding of the molecular basis of biology and disease.

描述（由申请人提供）：蛋白质结构倡议（PSI）知识库。我们建议创建一个名为结构生物学知识库（SBKB）的信息库和门户网站，这将是当前结构基因组学知识库（SGKB）的增强版本。SBKB将整合PSI：生物学中心的产品与外部数据库和社区输入的数据，在结构基因组学目标跟踪数据库TargetDB和蛋白质结构存储库protein data Bank中提供有关所有蛋白质序列的全面序列、结构和功能信息。此外，我们将继续与自然出版集团合作，提供有关结构生物学和基因组学的所有信息的“门户”。SGKB已将PSI工作的产品组织为七个模块（实验数据跟踪、技术、材料、建模、注释、出版物和度量），以便所有生物学和生物医学研究人员都可以从一个中央“一站式商店”访问这些信息。在本建议中，我们描述了增强现有模块的计划，并提出了一种新的格式，将底层SBKB数据组织为四个分类视图：目标、方法、结构-序列-函数和模型中心。这种方法通过向用户提供信息的集中视图，改进了当前的单界面方法。我们还在开发一种数据可视化工具，使用户可以动态地探索SBKB数据中的关系，从而创建新的假设。SBKB将在协调PSI：生物学网络的活动以及与不同生物领域的联系方面发挥重要作用。现有系统将用于协调PSI：生物网络参与者的内部通信。为了增加社区参与，我们描述了最近对社区提名目标系统的改进，并提出了一个新的web工具，用于收集社区对结构和目标的注释，并支持协作。我们的目标是使SBKB成为所有生物和生物医学社区的引人入胜和广泛使用的资源。