Tutorial on Protein Ontology Resources
Tutorial on Protein Ontology Resources
复制标题
DOI：
10.1007/978-1-4939-6783-4_3
复制
发表时间：
2017-01-01
期刊：
影响因子：
--
通讯作者：
Natale, Darren A.
中科院分区：
文献类型：
--
作者：
Arighi, Cecilia N.;Drabkin, Harold;Natale, Darren A.
蛋白质本体 (PRO) 是开放生物医学本体 (OBO) 铸造厂中蛋白质的参考本体，由代表同源基因、蛋白质形式（例如剪接同种型、序列变体和翻译后修饰形式）和蛋白质复合物的蛋白质类别的三个子本体组成。 PRO 定义了蛋白质和蛋白质复合物的类别，包括物种特异性和物种非特异性，并在分层框架中指示它们的关系，支持在适当的粒度级别进行准确的蛋白质注释、跨物种的蛋白质保守性分析以及语义推理。在本章的第一节中，我们描述了 PRO 框架，包括 PRO 术语的类别以及 PRO 与其他本体和蛋白质资源的关系。接下来，我们提供有关 PRO 网站 (proconsortium.org) 的教程，用户可以在其中浏览和搜索 PRO 层次结构、查看有关各个 PRO 术语的报告，并在分层表视图、多序列比对视图和 Cytoscape 网络视图中可视化 PRO 术语之间的关系。最后，我们描述了几个示例，说明 PRO 中可用的独特且丰富的信息。
The Protein Ontology (PRO) is the reference ontology for proteins in the Open Biomedical Ontologies (OBO) foundry and consists of three sub-ontologies representing protein classes of homologous genes, proteoforms (e.g., splice isoforms, sequence variants, and post-translationally modified forms), and protein complexes. PRO defines classes of proteins and protein complexes, both species-specific and species nonspecific, and indicates their relationships in a hierarchical framework, supporting accurate protein annotation at the appropriate level of granularity, analyses of protein conservation across species, and semantic reasoning. In the first section of this chapter, we describe the PRO framework including categories of PRO terms and the relationship of PRO to other ontologies and protein resources. Next, we provide a tutorial about the PRO website (proconsortium.org) where users can browse and search the PRO hierarchy, view reports on individual PRO terms, and visualize relationships among PRO terms in a hierarchical table view, a multiple sequence alignment view, and a Cytoscape network view. Finally, we describe several examples illustrating the unique and rich information available in PRO.