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）：“微生物遗传学的可怕力量”是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。对数千种细菌基因组和宏基因组中微生物表型的系统分析将通过一个通用系统来加强，以比较不同物种和菌株的表型。该项目的总体目标是建立这样一个系统，用于基于本体的微生物表型注释，这将使相关数据的有效挖掘，以促进，并可能有一天自动化，假设生成导致实验研究。根据该项目的第一笔赠款， 微生物表型（OMP）的建立，迄今已被用于注释大肠杆菌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;继续开发OMP注释所需的证据本体中的术语;开发一个管道，用于生成基于同线性的等位基因数据库和种内直系同源群（“泛基因”）;继续改进OMP网络/数据库基础设施;继续并扩大E.大肠杆菌;开始注释酿酒酵母;并参与社区推广。OMP正在多个项目的背景下开发，以改善生命所有领域的表型注释。由于OMP包含了一些研究得最好的模型遗传系统，因此它能够影响整个表型分析领域的方向。该项目将促进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都很有用。