The Protein Structure Inittiative Knowledgebase

蛋白质结构倡议知识库

• 批准号: 7896028
• 负责人: Helen M Berman
• 金额: $ 245.59万
• 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/7896028
• 关键词: Amino Acid Sequence; Biological; Biology; Collaborations; Communication; Communities; Data; Databases; Discipline; Disease; Educational workshop; Foundations; Genomics; Goals; Imagery; Internet; Methods; Metric; Modeling; Molecular; Nature; Participant; Peptide Sequence Determination; Play; Process; Protein Structure Initiative; Proteins; Publications; Published Comment; Publishing; Research Personnel; Resources; Role; Structure; System; Technology; Theoretical model; base; design; distributed data; improved; knowledge base; member; news; outreach; protein structure; public health relevance; repository; structural biology; structural genomics; symposium; tool

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(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)的信息库和网络门户，它将是当前结构基因组学知识库(SGKB)的增强版本。SBKB将把PSI：生物中心的产品与来自外部数据库和社区输入的数据相结合，以提供关于结构基因组目标跟踪数据库TargetDB和蛋白质结构储存库蛋白质数据库中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，为所有关于结构生物学和基因组学的信息提供一个“门户”。SGKB已将PSI工作的产品组织成七个模块(实验数据跟踪、技术、材料、建模、注释、出版物和度量)，以便所有生物和生物医学研究人员可以从中央“一站式商店”获取这些信息。在这个提案中，我们描述了我们对现有模块进行增强的计划，并提出了一种新的格式，将基础SBKB数据组织成四个分类视图：目标、方法、结构-序列-功能和模型中心。这种方法改进了当前的单一界面方法，为用户提供了集中的信息视图。我们还在开发一种数据可视化工具，该工具允许用户动态探索SBKB数据中的关系，从而能够创建新的假设。SBKB将在整个PSI：生物学网络的活动协调中发挥重要作用，并在拓展不同生物学领域方面发挥重要作用。现有系统将用于协调PSI：生物网络参与者的内部通信。为了增加社区的参与，我们描述了社区提名目标系统的最新增强，并提出了一个新的网络工具，该工具收集社区对结构和目标的注释，并使协作成为可能。我们的目标是使SBKB成为所有生物和生物医学社区的一个有吸引力和广泛使用的资源。 公共卫生相关性：结构生物学知识库将促进和简化来自各种生物学学科的用户获取蛋白质序列、结构和功能信息的途径。这样，就有可能对生物学和疾病的分子基础有广泛和深入的了解。