National Metabolomics Data Repository - nextgen Metabolomics Workbench

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

• 批准号: 10202576
• 负责人: Shankar Subramaniam
• 金额: $ 300.92万
• 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 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10202576
• 关键词: Biochemical Pathway; Biological; Biomedical Research; Cells; Cloud Service; Collaborations; Communication; Communities; Community Participation; Consultations; Data; Data Analyses; Data Display; Data Store; 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 repository; data reuse; data sharing; data standards; data tools; design; development policy; member; metabolome; metabolomics; metabolomics resource; metadata standards; 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.

抽象的 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 数据存储库建立在公平原则的基础上，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，我们开发了这样的第一个版本 存储库，称为代谢组学工作台（MW），我们通过该提案的总体努力将 下一代MW的开发如下： - 支持基于开放访问公共领域关系的最先进的数据库基础设施 数据库 PostGreSQL，将容纳与代谢组学相关的所有元数据和数据。 - 建立社区可接受的元数据和数据标准并制定更新的标准，其中 在专家界和其他利益相关者的帮助下，解决了缺乏的问题。 - 提供多个易于用户界面和多种格式选项，供研究人员输入所有元数据 以及与代谢组学研究相关的数据。 - 开发接口和工具，以便于查询和分析数据以及应用程序 用于添加/扩展现有工具和接口的程序员接口 (API)。 - 与 SEPCC 协商，生成用于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 和其他机构协调 利益相关者确保实现 NIH 代谢组学联盟的广泛目标。 - 制定让大量社区参与新兴代谢组学资源的机制 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，其职责是总体 协调，包括所有 NMDR 核心的管理以及制定指导方针 与所有其他利益相关者协调； b) 数据存储核心，它将容纳所有代谢组学数据， 提供一整套工具并提供用于在网络上查询、分析和显示数据的接口 被称为下一代 MW 的门户界面，并鼓励更广泛的社区存储数据； c) 的 治理核心将与 SEPCC 一起建立一个由 8 名专家组成的机构（其中 4 名是由 PI）为 NMDR 提供关于格式、协议和工具选择的深入指导； d) 额外的 核心，称为数据服务核心，这将是长期稳定性的先兆。这个前瞻性的 Core 将通过将下一代 MW 移植到混合云环境中来装备 NMDR，并 为基于云的代谢组学分析工具开发社区支持的容器技术。

项目成果

Phospholipase D3 degrades mitochondrial DNA to regulate nucleotide signaling and APP metabolism.

• DOI: 10.1038/s41467-023-38501-w
• 发表时间: 2023-05-24
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Van Acker, Zoe P.;Perdok, Anika;Hellemans, Ruben;North, Katherine;Vorsters, Inge;Cappel, Cedric;Dehairs, Jonas;Swinnen, Johannes V.;Sannerud, Ragna;Bretou, Marine;Damme, Markus;Annaert, Wim
• 通讯作者: Annaert, Wim

Chaperonin CCT controls extracellular vesicle production and cell metabolism through kinesin dynamics.

• DOI: 10.1002/jev2.12333
• 发表时间: 2023-06
• 期刊: Journal of extracellular vesicles
• 影响因子: 16

Targeting malaria parasites with novel derivatives of azithromycin.

• DOI: 10.3389/fcimb.2022.1063407
• 发表时间: 2022
• 期刊: Frontiers in cellular and infection microbiology
• 影响因子: 5.7

A nested case-control study of untargeted plasma metabolomics and lung cancer among never-smoking women within the prospective Shanghai Women's Health Study.

• DOI: 10.1002/ijc.34929
• 发表时间: 2024-04
• 期刊: International Journal of Cancer
• 影响因子: 6.4
• 作者: Mohammad L. Rahman;Xiao-Ou Shu;Dean P Jones;Wei Hu;B. Ji;Batel Blechter;Jason Y Y Wong-Jason-Y-Y-Wong-2290867708;Q. Cai-Q

Lipidomics dataset of PTEN deletion-induced optic nerve regeneration mouse model.

• DOI: 10.1016/j.dib.2020.106699
• 发表时间: 2021-03
• 期刊: Data in brief
• 影响因子: 1.2
• 作者: Arcuri J;Hegarty S;He Z;Bhattacharya SK
• 通讯作者: Bhattacharya SK