An Ontology for Bacterial Phenotypes

细菌表型本体论

• 批准号: 8052891
• 负责人: JAMES C HU
• 金额: $ 22.41万
• 依托单位: TEXAS A&M UNIVERSITY
• 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 2013-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8052891
• 关键词: Alleles; Antibiotics; Area; Awareness; Bacteria; Bacterial Model; Basic Science; Biological; Biological Models; Biological Process; Biology; Biotechnology; Cataloging; Catalogs; Cell physiology; Characteristics; Chemicals; Clinical Microbiology; Code; Communicable Diseases; Communities; Controlled Vocabulary; Custom; Databases; Development; Drug resistance; Education; Education and Outreach; Educational Curriculum; Escherichia coli; Evolution; Foundations; Gene Targeting; Generations; Genes; Genetic; Genome engineering; Genotype; Goals; Graduate Education; Health; Human; Internet; Link; Liquid substance; Literature; Methods; Microbe; Microbiology; Mission; Modeling; Molecular; Molecular Genetics; Mutation; Ontology; Organism; Pathogenesis; Persons; Phenotype; Pilot Projects; Process; Protocols documentation; Research Infrastructure; Research Personnel; Resources; Site; System; Terminology; Testing; United States National Institutes of Health; Variant; Virulence; base; biomedical ontology; comparative; comparative genomics; functional genomics; genome sequencing; improved; interest; metagenomic sequencing; microbial; microbial community; mutant; outreach; protein function; public health relevance; tool; trait; web site; wiki

DESCRIPTION (provided by applicant): Genome and metagenome sequencing efforts are producing a wealth of new information about microbes. Phenotypes are the observable traits resulting from genotypes and thus are a fundamental aspect of the biology of all organisms. Our ability to fully exploit the power of phenotypes for functional and comparative genomics in basic, applied, and clinical microbiology is hindered by the lack of a controlled terminology to describe and classify them. Ontologies are controlled vocabularies with defined relationships between terms. The overall goal of this project is to build a system for ontology-based annotation of bacterial phenotypes. The project will develop the necessary components and infrastructure, test the system on a well-characterized model system, and involve the relevant scientific communities in its development. The components are: 1) an Ontology for Microbial Phenotypes (OMP). 2) An extension of an existing ontology, the Evidence Code Ontology (ECO) to describe how OMP phenotypes were determined and cross referencing of ECO terms to a methods resource. 3) A pilot project to use the system to catalog phenotypes of mutations from E. coli, a well- understood bacterial model system. 4) a web site to help the scientific community find these new resources for bacterial phenotype annotation. 5) Outreach and education to promote the use of the system and to incorporate it into undergraduate and graduate education in genetics and microbiology. PUBLIC HEALTH RELEVANCE: An improved phenotype annotation system will have broad impacts relevant to the mission of NIH. The ability to correlate differences in gene content with important phenotypic differences between strains or microbial communities can help researchers target genes or organisms likely to be involved in virulence, drug resistance, and other important processes to infectious disease and human health. In addition, it can be used to elucidate the function of proteins involved in pathogenesis through comparative analysis based on phenotypes.

描述(由申请人提供)：基因组和元基因组测序工作正在产生大量关于微生物的新信息。表型是由基因类型产生的可观察到的特征，因此是所有生物体生物学的一个基本方面。由于缺乏描述和分类的受控术语，我们在基础、应用和临床微生物学中充分利用功能基因组学和比较基因组学表型的能力受到阻碍。本体是具有术语之间定义的关系的受控词汇表。这个项目的总体目标是建立一个基于本体的细菌表型注释系统。该项目将开发必要的部件和基础设施，在具有良好特点的模型系统上测试该系统，并让相关科学界参与其开发。这些组件包括：1)微生物表型本体论(OMP)。2)现有本体的扩展，即证据代码本体(ECO)，用于描述OMP表型是如何确定的，并将ECO术语交叉引用到方法资源。3)一个试点项目，使用该系统对大肠杆菌的突变表型进行分类，这是一个众所周知的细菌模型系统。4)一个网站，帮助科学界找到这些细菌表型注释的新资源。5)推广该系统的使用，并将其纳入遗传学和微生物学的本科生和研究生教育。 公共卫生相关性：改进的表型注释系统将对NIH的使命产生广泛的影响。将基因含量的差异与菌株或微生物群落之间的重要表型差异相关联的能力，可以帮助研究人员瞄准可能参与毒力、耐药性和其他感染疾病和人类健康的重要过程的基因或生物。此外，它还可以通过基于表型的比较分析来阐明参与发病的蛋白质的功能。