Extension of the Sequence Ontology: Preparing for the (re) sequencing revolution

序列本体的扩展：为（重新）测序革命做准备

• 批准号: 8462288
• 负责人: Karen Louise Eilbeck
• 金额: $ 28万
• 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 2016-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8462288
• 关键词: Adoption; Animal Model; Biological; Biology; Computer software; Data; Data Set; Development; Ensure; Eye; Funding; Genes; Genome; Genomics; Goals; Human Genome; Information Management; Ontology; Organism; Output; Process; Property; Publications; Publishing; Quality Control; Research; Research Personnel; Resources; Structure; Techniques; Technology; Terminology; Time; United States National Institutes of Health; Validation; Variant; Work; base; biomedical informatics; biomedical ontology; data management; file format; genome annotation; genome sequencing; information organization; meetings; novel; success; tool

DESCRIPTION (provided by applicant): High throughput sequencing technologies have made possible both personal human genome sequencing and rapid re-sequencing of many organisms. The dramatic increase in the throughputs of these technologies demands equal progress in the technologies used to manage their outputs. Over the last decade ontologies have emerged as indispensible tools for the management of large biomedical datasets. The Sequence Ontology (SO) is world's most widely used ontology for describing sequence annotations. The advent of rapid genome re-sequencing has made it essential that SO also provide the means to describe sequence variants. This renewal submission thus has two broad goals: (1) extend SO into the realm of genomic variant annotation, and (2) harmonize SO with recent developments in the field of biomedical ontology and genomics. Both are essential if we are to meet the data management needs of researchers seeking to exchange, compare and analyze re-sequenced genomes and their variants in the context of existing gene annotations.

描述(申请人提供)：高通量测序技术使个人人类基因组测序和许多生物的快速重新测序成为可能。要大幅提高这些技术的产量，就需要在用于管理其产出的技术方面取得同样的进展。在过去的十年里，本体论已经成为管理大型生物医学数据集不可或缺的工具。序列本体(Sequence Ontology，SO)是世界上使用最广泛的描述序列标注的本体。快速基因组重测序的出现使得提供描述序列变异的手段变得至关重要。因此，这次更新提交有两个广泛的目标：(1)将其扩展到基因组变异注释领域，以及(2)使其与生物医学本体论和基因组学领域的最新发展相协调。如果我们要满足研究人员在现有基因注释的背景下交换、比较和分析重新测序的基因组及其变体的数据管理需求，两者都是必不可少的。

项目成果

Quantitative measures for the management and comparison of annotated genomes.

• DOI: 10.1186/1471-2105-10-67
• 发表时间: 2009-02-23
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Eilbeck K;Moore B;Holt C;Yandell M
• 通讯作者: Yandell M

A proposed clinical decision support architecture capable of supporting whole genome sequence information.

提出的临床决策支持架构能够支持全基因组序列信息。

• DOI: 10.3390/jpm4020176
• 发表时间: 2014
• 期刊: Journal of personalized medicine
• 作者: Welch,BrandonM;Loya,SalvadorRodriguez;Eilbeck,Karen;Kawamoto,Kensaku
• 通讯作者: Kawamoto,Kensaku

GFVO: the Genomic Feature and Variation Ontology.

GFVO：基因组特征和变异本体。

• DOI: 10.7717/peerj.933
• 发表时间: 2015
• 期刊: PeerJ
• 影响因子: 2.7
• 作者: Baran,Joachim;Durgahee,BibiSehnaazBegum;Eilbeck,Karen;Antezana,Erick;Hoehndorf,Robert;Dumontier,Michel
• 通讯作者: Dumontier,Michel