National Metabolomics Data Repository - nextgen Metabolomics Workbench

摘要 这项提议的主要目标是建立一个强大的、基于云的国家代谢组学 建立在公平原则基础上的数据存储库，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，我们开发了第一个版本的这种 存储库，称为代谢组学工作台(MW)，以及我们通过这项提案所做的总体努力将 下一代兆瓦的发展如下： -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，它将存储与代谢组学有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攸关方的帮助下，缺乏。 -提供多种简单易用的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。 -开发界面和工具，方便用户查询和分析数据以及应用程序 程序员接口(API)，用于添加/扩展现有工具和接口。 -与SEPCC协商，为工具集成生成最佳实践协议和API。 -与代谢组学指导委员会、理事会、SEPCC和其他机构协调 利益攸关方确保实现NIH代谢组学联盟的广泛目标。 -制定机制，让非常大的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，其职责将是总体 协调，包括管理所有NMDR核心和制定指导方针 与所有其他利益攸关方协调；b)数据储存库核心，将存放所有代谢组学数据， 提供一大套工具并提供用于在Web上查询、分析和显示数据的界面 门户界面称为NextGen MW，并鼓励更广泛的社区存放数据；c) 治理核心，它将与SEPCC一起建立一个由八名专家组成的机构(由 PI)就格式、协议和工具的选择向NMDR提供深入指导；以及d)额外的 核心，称为数据服务核心，这将是长期稳定的先兆。这是前瞻性的 Core将通过将NextGen 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。

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.