Chibucos Marcus C, Zweifel Adrienne E, Herrera Jonathan C, Meza William, Eslamfam Shabnam, Uetz Peter, Siegele Deborah A, Hu James C, Giglio Michelle G
Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA.
Department of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX, USA.
BMC Microbiol. 2014 Nov 30;14:294. doi: 10.1186/s12866-014-0294-3.
Phenotypic data are routinely used to elucidate gene function in organisms amenable to genetic manipulation. However, previous to this work, there was no generalizable system in place for the structured storage and retrieval of phenotypic information for bacteria.
The Ontology of Microbial Phenotypes (OMP) has been created to standardize the capture of such phenotypic information from microbes. OMP has been built on the foundations of the Basic Formal Ontology and the Phenotype and Trait Ontology. Terms have logical definitions that can facilitate computational searching of phenotypes and their associated genes. OMP can be accessed via a wiki page as well as downloaded from SourceForge. Initial annotations with OMP are being made for Escherichia coli using a wiki-based annotation capture system. New OMP terms are being concurrently developed as annotation proceeds.
We anticipate that diverse groups studying microbial genetics and associated phenotypes will employ OMP for standardizing microbial phenotype annotation, much as the Gene Ontology has standardized gene product annotation. The resulting OMP resource and associated annotations will facilitate prediction of phenotypes for unknown genes and result in new experimental characterization of phenotypes and functions.
表型数据通常用于阐明适合进行基因操作的生物体中的基因功能。然而，在本研究之前，尚无用于细菌表型信息结构化存储和检索的通用系统。
已创建微生物表型本体（OMP）以规范从微生物中获取此类表型信息。OMP建立在基础形式本体和表型与性状本体的基础之上。术语具有逻辑定义，有助于对表型及其相关基因进行计算搜索。可通过维基页面访问OMP，也可从SourceForge下载。正在使用基于维基的注释捕获系统对大肠杆菌进行OMP的初始注释。随着注释工作的推进，新的OMP术语也在同步开发。
我们预计，研究微生物遗传学及相关表型的不同群体将采用OMP来规范微生物表型注释，就像基因本体对基因产物注释进行了标准化一样。由此产生的OMP资源及相关注释将有助于预测未知基因的表型，并带来对表型和功能的新实验表征。
