An Ontology for Microbial Phenotypes

描述(申请人提供)：“微生物遗传学令人敬畏的力量”是基于遗传学家从突变的表型推断复杂生物系统的组成和性质的能力。数以千计的细菌基因组和亚基因组中的微生物表型的系统分析将被一个通用的系统加强，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基于本体的微生物表型注释系统，使相关数据的有效挖掘能够促进并可能有一天自动生成导致实验研究的假设。在这个项目的第一笔拨款下， 建立了微生物表型(OMP)，到目前为止已经用来注释了大肠杆菌K-12中30%的基因。这项申请中提议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注释所需，继续开发证据本体论中的术语；开发用于生成基于同义词的等位基因和种内直系同源组(“Pangenes”)数据库的管道；继续改进OMP网络/数据库基础设施；继续和扩大在大肠杆菌中的注释工作；开始对酿酒酵母进行注释；以及参与社区外展。OMP是在多个项目的背景下开发的，以改善生活中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，它能够影响整个表型分析领域的方向。该项目将促进用于表型分析的生物信息学工具的发展，这将在所有遗传学领域都有用。

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.