The Protein Structure Initiative Knowledgebase

蛋白质结构倡议知识库

• 批准号: 9043658
• 负责人: Helen M Berman
• 金额: $ 1万
• 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 2017-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9043658
• 关键词: Amino Acid Sequence; Biological; Biology; Collaborations; Communication; Communities; Data; Databases; Discipline; Disease; Educational workshop; Foundations; Goals; Health; Imagery; Internet; Methods; 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; data visualization; design; distributed data; improved; knowledge base; member; news; outreach; protein structure; repository; structural biology; structural genomics; symposium; tool

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 ofthe 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 willcontinue 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 ofthe 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 ofthe 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 PSLBiology 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. RELEVANCE (See instructions): 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.

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”的信息库和门户网站 知识库（SBKB），这将是当前结构基因组学的增强版本 知识库（SGKB）。 SBKB 将整合 PSI 的产品：生物学中心的数据 外部数据库和社区输入提供全面的序列、结构和功能 有关所有蛋白质序列的信息 在结构基因组目标跟踪数据库 TargetDB 中 蛋白质结构存储库，蛋白质数据库。此外，我们将继续与 自然出版集团为所有有关结构生物学和基因组学的信息提供“门户”。 SGKB 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、出版物和指标），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，我们描述了我们的 计划增强现有模块，并提出一种新的格式来将底层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 该方法通过为用户提供集中的视图来改进当前的单一界面方法 信息。我们还在开发数据可视化工具，使用户能够 动态探索 SBKB 数据中的关系以创建新假设。 SBKB 将在协调 PSI：生物学网络和 涉足不同的生物领域。现有系统将用于协调内部通信 适用于 PSLBiology 网络参与者。为了增加社区参与，我们描述了最近的一项 增强社区提名的目标系统，并提出一个新的网络工具来收集 结构和目标的社区注释并实现协作。我们的目标是 SBKB 成为所有生物和生物医学界有吸引力且广泛使用的资源。 相关性（参见说明）： 结构生物学知识库将促进和简化对蛋白质序列、结构和蛋白质的获取 为来自各种生物学科的用户提供功能信息。通过这种方式，将有可能获得 对生物学和疾病的分子基础有广泛而深入的了解。