Novel Web-based Tools for Collaborative Community-Driven Genome Feature Annotatio

用于协作社区驱动的基因组特征注释的基于网络的新型工具

• 批准号: 8060606
• 负责人: Suzanna E Lewis
• 金额: $ 62.1万
• 依托单位: UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-01 至 2014-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8060606
• 关键词: Address; Biological; California; Characteristics; Client; Collaborations; Communities; Computer software; DNA; DNA Sequence; Data; Data Set; Databases; Documentation; Elements; Enhancers; Ensure; Generations; Generic Drugs; Genes; Genetic; Genome; Genomics; Goals; Grant; Human Genome; Indium; Individual; Internet; Knowledge; Laboratories; Laboratory Research; Life; Location; Mediation; Online Systems; Ontology; Organism; Process; Protocols documentation; RNA; Regulation; Reporting; Research Infrastructure; Research Personnel; Resolution; Resources; Site; Specific qualifier value; Structure; System; Technology; Testing; United States National Institutes of Health; Universities; Ursidae Family; Work; base; cyber infrastructure; data exchange; experience; flexibility; genome sequencing; graphical user interface; improved; interest; novel; outreach; promoter; public health relevance; skills; software development; tool; web page

DESCRIPTION (provided by applicant): This project's overarching aim is to develop a flexible and extensible infrastructure that will allow the entire community of a given organism to easily contribute to the genome annotation process. We are doing this by integrating and significantly enhancing the functionality existing GMOD tools: Apollo, used for the creation of genomic feature annotations tied to specific locations on the DNA sequence; the Distributed Annotation System (DAS) protocol and associated software, which supports the exchange of annotations over the Internet between researchers; and Generic Genome Browser (GBrowse), used for displaying genome annotations on interactive Web pages. We are combining these applications and building on them to create a novel web-based infrastructure that will offer robust, easy-to-use tools for collaborative, community-driven genome feature annotation by a much broader community of users. PUBLIC HEALTH RELEVANCE: As the number of whole genomes being sequenced increases the annotation of these genomes-what genes are present, the locations of promoter and enhancer sites, and other features-has become the rate-limiting step. Current annotations are unreliable, difficult to compare, and in some cases non-existent. This has serious consequences, because it diminishes the utility of these genome sequences, particularly as they are used for improving the standard of annotation of the human genome which is essential for its maximal exploitation.

描述（由申请人提供）：该项目的总体目标是开发一个灵活和可扩展的基础设施，使给定生物体的整个社区能够轻松地为基因组注释过程做出贡献。我们正在通过整合和显著增强现有GMOD工具的功能来做到这一点：Apollo，用于创建与DNA序列上特定位置相关的基因组特征注释;分布式注释系统（DAS）协议和相关软件，支持研究人员之间通过互联网交换注释;和通用基因组浏览器（GBrowse），用于在交互式网页上显示基因组注释。我们正在结合这些应用程序，并在其基础上创建一个新的基于网络的基础设施，将提供强大的，易于使用的工具，协作，社区驱动的基因组特征注释由更广泛的用户社区。 公共卫生关系：随着被测序的全基因组数量的增加，这些基因组的注释（存在哪些基因、启动子和增强子位点的位置以及其他特征）已成为限速步骤。目前的注释是不可靠的，难以比较，在某些情况下根本不存在。这具有严重的后果，因为它降低了这些基因组序列的效用，特别是当它们用于改进人类基因组的注释标准时，这对于其最大化利用是必不可少的。