Softward to facilitate adoption of the Sequence Ontology for genome management

Softward 促进采用序列本体进行基因组管理

• 批准号: 7234625
• 负责人: Karen Louise Eilbeck
• 金额: $ 17万
• 依托单位: UNIVERSITY OF UTAH
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-08-15 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7234625
• 关键词: Adopted; Adoption; Algorithms; Alternative Splicing; Animal Model; Base Sequence; Bioinformatics; Biological; Code; Communities; Computer software; Controlled Vocabulary; Data; Data Storage and Retrieval; Databases; Documentation; Ensure; Exons; Future; Gene Structure; Generations; Generic Drugs; Genes; Genetic; Genome; Genomics; Goals; Human; Introns; Investigation; Knowledge; Label; Libraries; Location; Manuals; Maps; Miso; Modeling; Nucleic Acid Regulatory Sequences; Occupations; Online Systems; Ontology; Output; Problem Solving; Process; Provider; Purpose; Quality Control; RNA Splicing; Resources; Scientist; Semantics; Services; Software Tools; Software Validation; Spliced Genes; Standards of Weights and Measures; Terminator Codon; Terminology; Testing; Transcript; Update; Validation; base; data modeling; day; file format; genome database; genome sequencing; human disease; improved; interoperability; model organisms databases; online tutorial; preference; structural genomics; syntax; tool

DESCRIPTION (provided by applicant): Genome annotations combine sequence, the results of bioinformatics analyses, and the knowledge of human curators into models of gene structure. These annotations provide a basic resource for investigations into the genetic causes of human disease. Despite their potential as a resource for such studies, genome annotations have proven difficult to use. A major reason for this has been the lack of community standards for describing them, which has resulted in the proliferation of arbitrary file formats and database schemas. In order to solve this problem, the Gene Ontology Consortium has developed the Sequence Ontology (SO). The purpose of SO is unify the description of genome annotations. Many model organism databases such as SGD, WormBase and FlyBase have now adopted SO, and release their annotations in SO-compliant formats. Many other genome databases are attempting to follow suite, but are finding it difficult to do so. One reason for their difficulties is the lack of publicly available software for managing and distributing SO- compliant genome annotations. The goal of this proposal is to further develop, improve and consolidate existing software tools that will help the broader genomics community to use the Sequence Ontology as a tool to produce, manage, and disseminate SO-compliant genome annotations. Our proposed data adapters and converters will help bring old annotation data and software forward; our SO-based quality control pipelines will ensure that the data produced by different databases is indeed interoperable; and our navigation and database search tools will help human curators to produce higher quality SO-compliant genome annotations.

描述（由申请人提供）：基因组注释结合了序列，生物信息学分析的结果以及人类策展人对基因结构模型的了解。这些注释为研究人类疾病的遗传原因提供了基本资源。尽管它们具有作为此类研究的资源的潜力，但已证明很难使用基因组注释。造成这种情况的主要原因是缺乏描述它们的社区标准，这导致了任意文件格式和数据库模式的扩散。为了解决这个问题，基因本体联盟已经开发了序列本体论（SO）。这样的目的是统一基因组注释的描述。许多模型生物数据库（例如SGD，Wormbase和Flybase）现在已经采用了SO，并以所谓的格式释放了注释。许多其他基因组数据库正在尝试遵循套件，但发现很难这样做。他们遇到困难的原因之一是缺乏用于管理和分发兼容的基因组注释的公开软件。该建议的目的是进一步开发，改进和巩固现有的软件工具，这将帮助更广泛的基因组学界使用序列本体论作为生产，管理和传播所谓基因组注释的工具。我们提出的数据适配器和转换器将有助于带来旧的注释数据和软件向前发展；我们基于如此基于的质量控制管道将确保不同数据库产生的数据确实可以互操作。我们的导航和数据库搜索工具将帮助人类策展人生成更高质量的所谓基因组注释。