A Data Coordinating Center for modENCODE

modENCODE 数据协调中心

• 批准号: 7617004
• 负责人: LINCOLN D. STEIN
• 金额: $ 115.53万
• 依托单位: ONTARIO INSTITUTE FOR CANCER RESEARCH
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-05-04 至 2011-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7617004
• 关键词: Age; Base Pairing; Binding Sites; Bioinformatics; Biological Process; Books; Caenorhabditis elegans; Chromatin; Code; Communities; Complex; Computers; Data; Data Coordinating Center; Data Files; Data Set; Databases; Deoxyribonuclease I; Development; Elements; Ensure; Eukaryota; Evolution; Familiarity; Genbank; Generic Drugs; Genes; Genome; Genomics; Goals; Human; Human Genome; Indium; Institutes; Knowledge; Mediating; Metadata; Methods; Modeling; Nucleotides; Pattern; Performance; Phase; Pilot Projects; Positioning Attribute; Procedures; Process; Production; Provider; Quality Control; RNA Splicing; Reading; Reagent; Reporting; Research; Research Personnel; Research Project Grants; Resources; Schedule; Scientist; Site; Sorting - Cell Movement; Source; Staging; Structure; System; Techniques; Testing; Tissues; Variant; Work; base; data mining; design; digital; experience; file format; fly; model organisms databases; open source; research study; software systems; technology development; tool

DESCRIPTION: The modENCODE project is a key sequel to the sequencing of the fly and worm genomes, and will have an enormous impact on our understanding of biological processes in all higher eukaryotes, including human. In order to manage the diverse, large-scale datasets that will be produced by modENCODE, we propose to create a data coordinating center (DCC) to track the data, integrate it with other information sources, and make it available to the research community in a timely and open fashion. This proposal brings together four groups with highly relevant backgrounds: The Micklem group, through its work on the InterMine system and FlyMine database, has extensive experience in integrating diverse types of data into high-performance data mining systems. The Stein and Lewis groups bring to the project an intimate familiarity with the C. elegans and D. melanogaster genomes, their reagents and research communities, and are well-positioned by their work with the WormBase and FlyBase databases to liaise with those MODs. The Kent group is responsible for the DCC for the Human ENCODE pilot project, and has extensive practical knowledge of developing and managing projects of this sort. We will assemble a team of three data managers stationed at CSHL and at Berkeley, who have a background in the bioinformatics of C. elegans and/or D. melanogaster. The managers will liaise with their contacts at the data provider sites to determine data file formats, milestones and quality control procedures for their datasets. They will also liaise with representatives from NCBI to coordinate modENCODE activities with the primary data repositories at GenBank and GEO. Data providers will upload their data sets to a staging server where they will be able to preview their data on an instance of the GBrowse genome browser. The data managers will QC the data before approving its transfer to the production database. Data will be integrated in the production database using InterMine, and from there released to the public on a monthly schedule. Researchers will be able to access the data via the GBrowse genome browser, bulk downloads, and via complex queries and reports mediated by InterMine and the BioMart data warehousing system. All major software systems used by the proposed DCC will be based on open source tools from the Generic Model Organism Database (GMOD), human ENCODE, and other sources. Throughout the project, Lewis and Stein will work close with FlyBase and/or WormBase to ensure that data collected by modENCODE becomes an integral part of the relevant model organism database. In addition we will dedicate a significant part of a data manager's effort to transfer data from modENCODE into the MODs during the last year of the project.

描述：modENCODE 项目是果蝇和蠕虫基因组测序的重要后续项目，将对我们对包括人类在内的所有高等真核生物的生物过程的理解产生巨大影响。为了管理 modENCODE 将产生的多样化、大规模数据集，我们建议创建一个数据协调中心（DCC）来跟踪数据，将其与其他信息源集成，并将其提供给研究界一种及时而开放的时尚。该提案汇集了四个具有高度相关背景的小组： Micklem 小组通过在 InterMine 系统和 FlyMine 数据库方面的工作，在将不同类型的数据集成到高性能数据挖掘系统中拥有丰富的经验。 Stein 和 Lewis 小组为该项目带来了对线虫和黑腹果蝇基因组、它们的试剂和研究群体的熟悉，并且通过与 WormBase 和 FlyBase 数据库的合作来与这些 MOD 进行联络，从而处于有利地位。 Kent 小组负责 Human ENCODE 试点项目的 DCC，并在开发和管理此类项目方面拥有丰富的实践知识。我们将组建一个由三名数据经理组成的团队，驻扎在 CSHL 和伯克利，他们拥有线虫和/或黑腹果蝇生物信息学的背景。管理人员将与数据提供者站点的联系人联络，以确定其数据集的数据文件格式、里程碑和质量控制程序。他们还将与 NCBI 的代表联络，协调 modENCODE 活动与 GenBank 和 GEO 的主要数据存储库。数据提供者将他们的数据集上传到临时服务器，他们将能够在 GBrowse 基因组浏览器实例上预览他们的数据。数据经理将在批准将数据传输到生产数据库之前对其进行质量控制。数据将使用 InterMine 集成到生产数据库中，并按月计划向公众发布。研究人员将能够通过 GBrowse 基因组浏览器、批量下载以及由 InterMine 和 BioMart 数据仓库系统介导的复杂查询和报告来访问数据。拟议的 DCC 使用的所有主要软件系统都将基于通用模型生物数据库 (GMOD)、人类 ENCODE 和其他来源的开源工具。在整个项目中，Lewis 和 Stein 将与 FlyBase 和/或 WormBase 密切合作，以确保 modENCODE 收集的数据成为相关模型生物数据库的组成部分。此外，在项目的最后一年，我们将投入大量数据管理人员的工作，将数据从 modENCODE 传输到 MOD。