National Metabolomics Data Repository - nextgen Metabolomics Workbench

国家代谢组学数据存储库 - nextgen Metabolomics Workbench

• 批准号: 9979851
• 负责人: Shankar Subramaniam
• 金额: $ 299.99万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-17 至 2022-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9979851
• 关键词: Biochemical Pathway; Biological; Biomedical Research; Cells; Cloud Service; Collaborations; Communication; Communities; Community Participation; Consultations; Data; Data Analyses; Data Display; Databases; Deposition; Development; Ensure; Environment; FAIR principles; Foundations; Functional disorder; Funding; Future; Goals; Governing Board; Guidelines; Human; Hybrids; Infrastructure; Life; Mass Spectrum Analysis; Measurable; Measurement; Metabolism; Metadata; Nuclear Magnetic Resonance; Phase; Phenotype; Physiology; Protocols documentation; Public Domains; Research; Research Personnel; Resource Sharing; Services; Solid; Techniques; Technology; Time; TimeLine; Tissues; United States National Institutes of Health; Work; base; cloud based; cloud platform; data reuse; data sharing; data standards; data tools; data warehouse; design; development policy; interoperability; member; metabolome; metabolomics; metabolomics resource; method development; next generation; outreach; portability; relational database; repository; tissue reconstruction; tool; web portal

Abstract The primary objective of this proposal is the establishment of a robust, cloud-based National Metabolomics Data Repository founded on the FAIR principle, i.e. findable, accessible, interoperable, and reusable with scalability, extensibility, and portability. Over the past six years, we have developed the first version of such a repository, known as the Metabolomics Workbench (MW), and our overarching effort through this proposal will be to develop the next generation MW as follows: - Support a state-of-the-art database infrastructure based on an open-access public domain relational database, PostGreSQL, which will house all metadata and data pertaining to metabolomics. - Establish community-acceptable metadata and data standards and develop newer standards, where lacking, with the aid of the expert community and other stakeholders. - Provide multiple easy-user interfaces with multiple format options for researchers to enter all metadata and data associated with a metabolomics study. - Develop interfaces and tools for easy access to querying and analyzing the data along with Application Programmer Interfaces (APIs) to add/extend existing tools and interfaces. - Generate, in consultation with the SEPCC, best practice protocols and APIs for tool integration. - Coordinate with the Metabolomics Steering Committee, the Governing Board, the SEPCC, and other stakeholders to ensure that the broad goals of the NIH Metabolomics Consortium are achieved. - Formulate mechanisms for very large community participation in burgeoning metabolomics resources and communicate to the larger biomedical community the value of using metabolomics data and tools for research. The proposed NMDR will have 4 cores, namely a) the Admin Core, whose responsibility will be the overall coordination, including the administration of all the NMDR cores and establishment of guidelines for coordination with all other stakeholders; b) the Data Repository Core, which will house all metabolomics data, provide a large suite of tools and provide interfaces for querying, analyzing, and displaying the data on a web portal interface known as the nextgen MW, and encourage the broader community to deposit data; c) the Governance Core, which will, along with the SEPCC, establish a body of eight experts (four recommended by the PI) to provide deep guidance to the NMDR for choice of formats, protocols, and tools; and d) an additional core, called the Data Services Core, which will be the harbinger for long-term stability. This forward-looking Core will equip the NMDR for the future by porting the nextgen MW into a hybrid cloud environment and developing a community-supported container technology for cloud-based metabolomics analysis tools.

摘要 该提案的主要目标是建立一个强大的，基于云的国家代谢组学 数据仓库建立在公平原则之上，即可查找、可访问、可互操作和可重用， 可伸缩性、可扩展性和可移植性。在过去的六年里，我们已经开发了这样一个 储存库，称为代谢组学实验室（MW），我们通过这项提案的总体努力将 开发下一代MW如下： - 支持基于开放访问公共领域关系数据库的最先进的数据库基础设施 数据库PostgreSQL，它将容纳所有与代谢组学有关的元数据和数据。 - 建立社区可接受的元数据和数据标准，并制定更新的标准， 在专家社区和其他利益攸关方的帮助下， - 为研究人员输入所有元数据提供具有多种格式选项的多个简单用户界面 以及与代谢组学研究相关的数据。 - 开发接口和工具，以便轻松访问查询和分析数据沿着应用程序 程序员接口（API），用于添加/扩展现有工具和接口。 - 与SEPCC协商，生成工具集成的最佳实践协议和API。 - 与代谢组学指导委员会，理事会，SEPCC和其他 利益相关者，以确保实现NIH代谢组学联盟的广泛目标。 - 制定机制，让大量社区参与新兴的代谢组学资源 并向更大的生物医学界传达使用代谢组学数据和工具的价值 用于研究 拟议的NMDR将有4个核心，即a）管理核心，其职责是全面 协调，包括所有NMDR核心的管理和建立指导方针， 与所有其他利益相关者的协调; B）数据存储库核心，它将容纳所有代谢组学数据， 提供了一个大型工具套件，并提供了用于查询、分析和在Web上显示数据的接口 门户接口称为下一代MW，并鼓励更广泛的社区存款数据; c） 治理核心，它将与SEPCC一起沿着建立一个由八名专家组成的机构（其中四名专家由 PI）为NMDR提供格式、协议和工具选择的深入指导;以及d）额外的 核心，称为数据服务核心，这将是长期稳定的预兆。这种前瞻性 Core将通过将下一代MW移植到混合云环境中， 为基于云的代谢组学分析工具开发社区支持的容器技术。