Microbiome Data Management Core (MDMC)

微生物组数据管理核心 (MDMC)

• 批准号: 8142194
• 负责人: Jennifer Russo Wortman
• 金额: $ 10.53万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8142194
• 关键词: Area; Bacterial Genome; Bioinformatics; Biological Models; Collaborations; Commit; Communication; Communities; Computer software; Data; Data Set; Data Storage and Retrieval; Databases; Development; Documentation; Electronic Mail; Electronics; Ensure; Epidemiology; Future; Gene Expression Profile; Genes; Genetic; Genomics; Goals; Housing; Human; Human Microbiome; Individual; Institutes; Institution; Internet; Meta-Analysis; Metadata; Metagenomics; Methods; Mind; Obesity; Patients; Phenotype; Reporting; Research; Resources; Retrieval; Ribosomal RNA; Sampling; Schedule; Scientist; Services; Shapes; Source Code; Statistical Methods; System; Technology; Training; Training Support; Update; Validation; Vision; base; comparative; data exchange; data management; data modeling; design; electronic data; experience; file format; flexibility; genome sequencing; meetings; microbial; microbial community; microbiome; open source; programs; repository; sample collection; success; web site; wiki

Core B,the Microbiome Data ManagementCore (MDMC), will serve as a central data repository for Projects 1, 2 and 3 as well as Core A. This facility will be housed at TIGR and directed by Jeremy Selengut of TIGR's Bioinformatics Department. The diverse data types and large amount of data that will be generated by the different components of this program necessitate a central facility for data storage and access. This typeof program, with a distributed sequencing effort, a shared pool of data for collaborative analysis, and a common database to flexibly represent not only the data but the growing conceptual model of the system under study, is likely to be an archetype of future human microbiome and other environmental metagenomics research. The plan we outline utilizes technologies and methods with which we are very experienced and skilled, but are combined and shaped into a new system optimized for this type of programmatic effort. There are 3 aims. Aim 1 Establish a Core Database. We will establish a database repository to support the sample collection effort and metagenomic/pan-genomic, analyses for the microbiome project. This system will support types of data critical to the success of this program project:e.g., subsets of de-identified patient metadata, 16SrRNA- pan-genomic- and fecal community microbiome gene, transcriptome and metabolite datasets). We will provision for multiple users and institutions to operate on the database, and develop straightforward electronic submission and retrieval mechanisms for the MDMC database. Aim 2: Formalize Data Exchange. The core will ensure that all electronic data are robustly encoded in a data exchange file format to effectively support the project. We will supply an Application Programmer Interface (API)that will allow all contributors to deliver data to MDMC over the web. We will support the API with documentation. Open Source code, training support, and validation scripts for all data required by the project. Aim 3: Maintain Communication Between the MDMC and Projects 1, 2 and 3. Ensuring mat the data management system meets the needs of the scientists distributed among the other projects in this proposal is paramount. This will be accomplished by development of documentation, a help desk system, direct contacts between key staff, a system of email updates, reports to the project website, and attendance at all regularly scheduled meetings.

核心B，即微生物组数据管理核心（MDMC），将作为项目的中央数据存储库 1、2和3以及核心A。该设施将设在TIGR，由TIGR的Jeremy Selengut负责指导 生物信息学系。将生成的各种数据类型和大量数据 该方案的不同组成部分需要一个用于数据存储和访问的中央设施。这类 程序，具有分布式测序工作，用于协作分析的共享数据池，以及 通用数据库不仅可以灵活地表示数据，还可以灵活地表示系统的不断增长的概念模型 正在研究中，可能是未来人类微生物组和其他环境微生物组的原型。 宏基因组学研究。我们概述的计划利用了我们非常熟悉的技术和方法。 经验丰富，技术熟练，但结合起来，形成一个新的系统，为这种类型的优化 方案努力。有三个目标。目标1建立核心数据库。我们会建立一个数据库 储存库，以支持样本收集工作和宏基因组/泛基因组分析， 微生物组项目。该系统将支持对该计划项目的成功至关重要的数据类型：例如， 去识别患者元数据的子集，16 SrRNA-泛基因组和粪便群落微生物组基因， 转录组和代谢物数据集）。我们将为多个用户和机构提供操作 数据库，并为MDMC开发简单的电子提交和检索机制 数据库目标2：使数据交换正规化。核心将确保所有电子数据都是可靠的， 以数据交换文件格式编码，以有效支持项目。我们将提供一个应用程序 程序员接口（API），允许所有贡献者通过网络向MDMC提供数据。我们将 使用文档支持API。所有数据的开源代码、培训支持和验证脚本 项目所需。目标3：保持MDMC与项目1、2和3之间的沟通。 确保数据管理系统满足分布在其他系统中的科学家的需求 在这个项目中，项目是至关重要的。这将通过开发文档来完成， 桌面系统，主要工作人员之间的直接联系，电子邮件更新系统，向项目网站提交报告，以及 出席所有定期会议。