Department of Genetics, University of Cambridge, Downing Street, Cambridge, Cambridge CB2 3EH, UK.
Bioinformatics. 2012 Jul 1;28(13):1783-9. doi: 10.1093/bioinformatics/bts250. Epub 2012 Apr 26.
The systematic observation of phenotypes has become a crucial tool of functional genomics, and several large international projects are currently underway to identify and characterize the phenotypes that are associated with genotypes in several species. To integrate phenotype descriptions within and across species, phenotype ontologies have been developed. Applying ontologies to unify phenotype descriptions in the domain of physiology has been a particular challenge due to the high complexity of the underlying domain.
In this study, we present the outline of a theory and its implementation for an ontology of physiology-related phenotypes. We provide a formal description of process attributes and relate them to the attributes of their temporal parts and participants. We apply our theory to create the Cellular Phenotype Ontology (CPO). The CPO is an ontology of morphological and physiological phenotypic characteristics of cells, cell components and cellular processes. Its prime application is to provide terms and uniform definition patterns for the annotation of cellular phenotypes. The CPO can be used for the annotation of observed abnormalities in domains, such as systems microscopy, in which cellular abnormalities are observed and for which no phenotype ontology has been created.
The CPO and the source code we generated to create the CPO are freely available on http://cell-phenotype.googlecode.com.
系统观察表型已成为功能基因组学的重要工具，目前有几个大型的国际项目正在进行中，旨在识别和描述与几种物种基因型相关的表型。为了在物种内和物种间整合表型描述，已经开发了表型本体。由于基础领域的高度复杂性，将本体应用于统一生理学领域的表型描述一直是一个特殊的挑战。
在这项研究中，我们提出了一个生理学相关表型本体的理论及其实现的大纲。我们提供了过程属性的形式描述，并将其与它们的时间部分和参与者的属性联系起来。我们应用我们的理论来创建细胞表型本体（CPO）。CPO 是细胞、细胞成分和细胞过程的形态和生理表型特征的本体。它的主要应用是为细胞表型的注释提供术语和统一的定义模式。CPO 可用于系统显微镜等领域的观察异常的注释，在这些领域中观察到细胞异常，但尚未创建表型本体。
CPO 和我们为创建 CPO 而生成的源代码可在 http://cell-phenotype.googlecode.com 上免费获得。
