Core B/C: Data & Dissemination

核心 B/C：数据

• 批准号: 7980195
• 负责人: JOHN A GERLT
• 金额: $ 39.36万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-05-20 至 2015-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7980195
• 关键词: Access to Information; Address; Advisory Committees; Apache Indians; Architecture; Archives; Area; Arts; Back; Bioinformatics; Biology; Charge; Chimera organism; Classification; Collaborations; Communication; Communities; Computer Analysis; Computer software; Custom; Data; Databases; Deposition; Development; Docking; Educational workshop; Ensure; Enzymes; Family; Funding; Funding Agency; General Practices; Genome; Genomics; Goals; Human Resources; Imagery; Individual; Information Dissemination; Information Technology; Institutes; Instruction; Internet; Laboratories; Libraries; Ligands; Link; Linux; Literature; Maintenance; Management Information Systems; Maps; Metadata; Methods; Modeling; Monitor; Monograph; Online Systems; Operating System; Peer Review; Protein Structure Initiative; Proteins; Protocols documentation; Publications; Publishing; Reagent; Reporting; Research; Research Methodology; Research Personnel; Resources; Review Literature; Scientific Societies; Screening procedure; Services; Site; Soaps; Specific qualifier value; Structural Models; Structure; Structure-Activity Relationship; System; Text; Update; Work; Zinc; base; comparative; cost; crosslink; data exchange; data portal; data sharing; data structure; database structure; design; experience; federated computing; feeding; graphical user interface; interest; material transfer agreement; meetings; member; news; online tutorial; outreach; research study; structural biology; tool; user-friendly; virtual; web page; web site

SUMMARY The Data and Dissemination Core [Babbitt (UCSF) and Buriey (Lilly), CoDirectors] addresses the requirements for data gathering/coordination, information dissemination, and bioinformatics as specified in the RFA for U54 Centers. This Core combines Cores B (Information Dissemination and Data-Coordinating Core) and C (Bioinformatics). For the Enzyme Function Initiative (EFI), the Data and Dissemination Core will be implemented and managed using four primary resources working together to ensure ease of data input and tracking by EFI members, coordination of experimental and computational data, implementation and access to analysis and visualization tools, and dissemination of data and information to EFI investigators and the public. Instructions for depositing data and information to the EFI and for using the tools and results of EFI efforts will be provided in the form of help files and online tutorials. Strategies and protocols for dissemination of EFI resources and materials, software and experimental results will also be provided by the core resources. Each is listed briefly below and described in detail in the sections following. EFI results will also be disseminated through publications in the peer-reviewed literature, presentations by EFI investigators at meetings and other venues, and through workshops developed for presentation at meetings of scientific societies and other appropriate organizations. 1. The EFI Website, the responsibility of the Administrative Core at UIUC (Gerit, Director), will be the official site for the EFI, providing information about the project and resources and acting as one of the portals for access to its data, results and materials. The homepage will provide tutorials, listings of publications, news, and other relevant information. Links will enable access to the Data Resource (Laboratory Information Management System for EFI members), the Structure Function Linkage Database, and the Computation Core (see sections 2-4 below). 2. The Data Resource (Sauder, Director) will rely on a state-of-the-art Laboratory Information Management System (LIMS) that has been optimized for high-throughput structural biology and studies of protein ligand-interactions. EFI experimental results and methods will be stored in the Data Resource for transfer to appropriate databases for dissemination. Target status will be automatically shared with the Structure Function Linkage Database (SFLD), together with other associated data. Structure and function results will be available through public websites linked to the Data Resource and through the other primary resources, including the EFI website and the SFLD. Because the core architecture of LIMS has already been implemented and its efficacy validated by a large numbers of users, this resource can provide extensive functionality at minimal cost to the EFI, with the requested funds used to extend LIMS to accommodate the specialized needs of the EFI and to integrate it with the other EFI resources described in this proposal. 3. The Structure Function Linkage Database (SFLD) (Babbitt, Director) will provide access to information about the superfamilies targeted by the Bridging Projects hierarchically classified by both sequence/structural and functional similarity into superfamilies and [monofunctional] families. Developed originally to analyze structure-function relationships of functionally diverse enzyme superfamilies, the SFLD will enable user access to EFI data and results in two major ways. First, the SFLD will serve as a continually updated archive of all sequences, structures (obtained experimentally or from models), and functions that are known for Bridging Project superfamilies, including functions discovered by the EFI Bridging Projects and Scientific Cores. Second, the SFLD will provide the results of computational (bioinformatic) and experimental analyses of these superfamilies in the context of their structure-function relationships to EFI investigators and the public. An extensive set of browse and search tools provide access to these data and information. Because the core architecture of the SFLD has already been implemented, EFI funds can be used principally to create new analysis and visualization functionality and to implement integration and sharing of data and information with the other dissemination resources. Computational analysis of superfamily structure-function relationships for target identification and function prediction is described in the Superfamily/Genome Core. 4. The Computation Core (Jacobson, Director) will create or extend existing resources to disseminate modeling and docking results along with relevant protocols and methods. As deemed useful, subsets of the raw data will be available for dissemination by LIMS or the SFLD and via links from the EFI Website. Because data and results are still closely tied to the further development of research methods, data coordination and bioinformatics for the Computation Core is described in that section rather than here. Only the dissemination and outreach efforts for the Computation Core are described in this Core proposal.

概括 数据和传播核心[Babbitt（UCSF）和Buriey（Lilly），Codirectors]解决了 RFA中指定的U54中心中指定的数据收集/协调，信息传播和生物信息学的要求。该核心结合了内核B（信息传播和数据协调核心）和C（生物信息学）。对于酶函数计划（EFI），将使用四个主要资源共同实施和管理数据和传播核心，以确保EFI成员的数据输入和跟踪，协调和计算数据的协调，实验和计算数据，实现和访问分析和可视化工具，以及向EFI研究者和公众传播数据以及信息以及信息和信息。 将以帮助文件和在线教程的形式提供有关将数据和信息存入EFI以及使用EFI努力的工具和结果的说明。核心资源也将提供传播EFI资源和材料，软件和实验结果的策略和协议。在下面简要列出了每个部分，并在下面的各节中进行详细描述。 EFI的结果还将通过同行评审文献中的出版物，EFI调查人员在会议和其他 场地，以及通过在科学社会和其他适当组织的会议上开发的研讨会。 1。EFI网站，UIUC的行政核心的责任（Gerit，董事）将是 EFI的官方网站，提供有关项目和资源的信息，并充当访问其数据，结果和材料的门户网站之一。首页将提供教程，出版物列表，新闻和其他相关信息。链接将使访问数据资源（EFI成员的实验室信息管理系统），结构功能链接数据库和计算核心（请参阅下面的第2-4节）。 2。数据资源（索德，董事）将依靠最先进的实验室信息 管理系统（LIM）已针对高通量结构生物学和蛋白质配体相互作用的研究进行了优化。 EFI实验结果和方法将存储在数据资源中，以传输到适当的数据库以进行传播。目标状态将与结构功能链接数据库（SFLD）一起自动共享，以及其他关联的数据。结构和功能结果将通过链接到数据资源的公共网站以及其他主要资源（包括EFI网站和SFLD）获得。由于LIMS的核心体系结构已经实施，并由大量用户验证其效力，因此该资源可以以最低的成本提供广泛的功能，而所请求的资金用于扩展LIMS，以扩展EFI的专业需求，并与此提案中描述的其他EFI资源集成在一起。 3。结构函数链接数据库（SFLD）（董事Babbitt）将提供对 有关桥接项目针对的超家族的信息， 序列/结构和功能相似性，分为超家族和[单功能]家族。 SFLD最初开发的旨在分析功能多样的酶超家族的结构 - 功能关系，将使用户访问EFI数据并以两种主要方式产生。首先，SFLD将作为所有序列，结构（实验或从模型中获得）的不断更新的存档，以及以桥接项目超家族而闻名的功能，包括EFI桥接项目和科学核心发现的功能。其次，SFLD将提供计算（生物信息学）和实验的结果 这些超家族在与EFI调查人员和公众的结构 - 功能关系的背景下进行分析。一组广泛的浏览和搜索工具可访问这些数据和信息。由于已经实施了SFLD的核心体系结构，因此可以将EFI资金主要用于创建新的分析和可视化功能，并与其他传播资源实施集成和共享数据和信息。超家族函数函数函数关系的计算分析在超家族/基因组核心中描述了目标识别和功能预测。 4。计算核心（主任雅各布森）将创建或扩展现有资源 传播建模和对接结果以及相关协议和方法。如认为有用的，原始数据的子集将用于LIMS或SFLD的传播以及通过EFI网站的链接。由于数据和结果仍然与研究方法的进一步开发密切相关，因此该节而不是此处描述了计算核心的数据协调和生物信息学。在本核心建议中仅描述了计算核心的传播和外展工作。