The Protein Structure Initiative Knowledgebase

蛋白质结构倡议知识库

• 批准号: 8692859
• 负责人: DAVID S GOODSELL
• 金额: $ 2.06万
• 依托单位: RUTGERS, THE STATE UNIV OF N.J.
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至 2017-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8692859
• 关键词: Amino Acid Sequence; Biological; Biology; Collaborations; Communication; Communities; Data; Databases; Discipline; Disease; Educational workshop; Foundations; Goals; Imagery; Instruction; 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; 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.

蛋白质结构倡议（PSI）知识基础 我们建议创建一个名为“结构生物学”的信息存储库和网络门户 知识库（SBKB），它将成为当前结构基因组学的增强版本 知识库（SGKB）。 SBKB将将PSI的产品集成：生物学中心与来自 外部数据库和社区输入，以提供全面的顺序，结构和功能 有关结构基因组学中所有蛋白质序列的信息目标跟踪数据库，targetDB和 蛋白质结构存储库，蛋白质数据库。此外，我们将与 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“网关”。 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，出版物和指标），以便所有生物学和生物医学 研究人员可以从中央的“一站式商店”访问此信息。在此提案中，我们描述了我们的 计划增强现有模块，并提出一种新格式，以将基础SBKB数据组织到 四个分类视图：目标，方法，结构 - 序列功能和模型中心。这 通过为用户提供重点视图，方法可以改善当前的单个接口方法 信息。我们还在开发一个数据可视化工具，该工具允许用户 动态探索SBKB数据中的关系，以实现新假设的创建。 SBKB将在PSI的活动协调中发挥重要作用：生物学网络和 与各种生物领域的宣传。现有系统将用于协调内部通信 用于PSLBIology网络参与者。为了增加社区的参与，我们描述了最近的一个 增强社区提名的目标系统，并提出一种新的网络工具来收集 结构和目标的社区注释可以合作。我们的目标是让SBKB 成为所有生物学和生物医学社区的引人入胜且广泛使用的资源。