An Ontology for Microbial Phenotypes

微生物表型本体论

• 批准号: 8579651
• 负责人: JAMES C HU
• 金额: $ 29.73万
• 依托单位: TEXAS A&M AGRILIFE RESEARCH
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-04-01 至 2017-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8579651
• 关键词: Adoption; Age; Alleles; Bacteria; Bacterial Genome; Bioinformatics; Characteristics; Clinical; Community Outreach; Controlled Vocabulary; Data; Data Storage and Retrieval; Databases; Development; Disease; Escherichia coli; Foundations; Generations; Genes; Genetic; Genotype; Goals; Grant; Health; Human; Individual; Internet; Life; Link; Microbial Genetics; Microbiology; Mining; Ontology; Organism; Orthologous Gene; Pattern; Phase; Phenotype; Positioning Attribute; Property; Research Infrastructure; Saccharomyces cerevisiae; Study models; Synteny; System; Terminology; Variant; Work; base; comparative; complex biological systems; data structure; fungus; genome sequencing; improved; metagenome; metagenomic sequencing; microbial; mutant; outreach; public health relevance; relational database; research study; tool; wiki

DESCRIPTION (provided by applicant): The "awesome power of microbial genetics" is based on the ability of geneticists to infer the components and properties of complex biological systems from the phenotypes of mutants. The systematic analysis of microbial phenotypes in thousands of bacterial genomes and metagenomes will be strengthened by a universal system to compare phenotypes across species and strains. The overall goal of this project is to build a such a system for ontology-based annotation of microbial phenotypes that will enable the efficient mining of relevant data to facilitate, and possibly one day automate, hypothesis generation leading to experimental studies. Under the first grant for this project, the Ontology of Microbial Phenotypes (OMP) was built and has so far been used to annotate 30% of the genes in Escherichia coli K-12. The work proposed in this application will develop and deploy a relational database for annotation data storage; continue development of the OMP; continue development of terms in the Evidence Ontology as needed for OMP annotation; develop a pipeline for generation of a synteny-based database of alleles and intraspecies ortholog groups ("pangenes"); continue improvement of the OMP web/database infrastructure; continue and expand annotation efforts in E. coli; begin annotation of Saccharomyces cerevisiae; and engage in community outreach. OMP is being developed in the context of multiple projects to improve phenotype annotation across all domains of life. As OMP encompasses some of the best-studied model genetic systems, it is in a position to influence the direction of the entire field o phenotype analysis. This project will stimulate the development of bioinformatics tools for phenotype analysis, which will be useful across all of genetics.

描述（由申请人提供）：“微生物遗传学的惊人力量”基于遗传学家从突变体的表型推断复杂生物系统的组成和特性的能力。对数千个细菌基因组和宏基因组中微生物表型的系统分析将通过比较物种和菌株表型的通用系统得到加强。该项目的总体目标是建立一个这样的系统，用于基于本体论的微生物表型注释，该系统将能够有效挖掘相关数据，以促进并可能有一天实现假设生成的自动化，从而导致实验研究。在该项目的第一笔资助下，本体论 微生物表型 (OMP) 已建立，迄今为止已用于注释大肠杆菌 K-12 中 30% 的基因。本申请中提出的工作将开发和部署用于注释数据存储的关系数据库；继续开发 OMP；根据 OMP 注释的需要，继续开发证据本体中的术语；开发用于生成等位基因和种内直向同源群（“pangenes”）的基于同线性的数据库的管道；继续改进 OMP 网络/数据库基础设施；继续并扩大大肠杆菌的注释工作；开始酿酒酵母的注释；并参与社区外展活动。 OMP 正在多个项目的背景下开发，以改善生命各个领域的表型注释。由于 OMP 涵盖了一些研究最充分的模型遗传系统，因此它能够影响整个表型分析领域的方向。该项目将刺激用于表型分析的生物信息学工具的开发，这将在所有遗传学领域发挥作用。