A Data Coordinating Center for modENCODE

产品说明： modENCODE项目是苍蝇和蠕虫基因组测序的关键续集，将对我们理解所有高等真核生物（包括人类）的生物过程产生巨大影响。为了管理modENCODE将产生的多样化的大规模数据集，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，并以及时和开放的方式提供给研究社区。这项建议汇集了四个背景高度相关的小组：Micklem小组通过其在InterMine系统和FlyMine数据库方面的工作，在将各种类型的数据纳入高性能数据挖掘系统方面拥有丰富的经验。Stein和刘易斯小组为这个项目带来了对C语言的熟悉。elegans和D.黑腹果蝇基因组，他们的试剂和研究社区，并通过他们与WormBase和FlyBase数据库的工作与这些MOD保持联系。肯特团队负责人类ENCODE试点项目的DCC，并拥有开发和管理此类项目的广泛实践知识。我们将组建一个由三名数据管理员组成的团队，分别驻扎在CSHL和伯克利，他们都有C的生物信息学背景。elegans和/或D.黑腹菌管理人员将与数据提供者所在地的联系人联络，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，以协调modENCODE与GenBank和GEO主要数据库的活动。数据提供者将把他们的数据集上传到一个临时服务器，在那里他们将能够在GBrowse基因组浏览器的实例上预览他们的数据。数据管理员将在批准将数据转移到生产数据库之前对数据进行质量控制。将使用InterMine将数据纳入生产数据库，并每月向公众公布。研究人员将能够通过GBrowse基因组浏览器访问数据，批量下载，并通过InterMine和BioMart数据仓库系统介导的复杂查询和报告。拟议DCC使用的所有主要软件系统将基于通用模式生物数据库（GMOD）、人类ENCODE和其他来源的开源工具。在整个项目中，刘易斯和斯坦将与FlyBase和/或WormBase密切合作，以确保modENCODE收集的数据成为相关模式生物数据库的组成部分。此外，在项目的最后一年，我们将投入数据管理人员的大量工作，将数据从modENCODE传输到MOD中。

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.