Arighi Cecilia N, Drabkin Harold, Christie Karen R, Ross Karen E, Natale Darren A
Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE, 19711, USA.
The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
Methods Mol Biol. 2017;1558:57-78. doi: 10.1007/978-1-4939-6783-4_3.
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.
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，由三个子本体组成，分别代表同源基因的蛋白质类别、蛋白质异构体（如剪接异构体、序列变体和翻译后修饰形式）以及蛋白质复合物。PRO定义了特定物种和非特定物种的蛋白质和蛋白质复合物类别，并在层次框架中表明它们之间的关系，支持在适当的粒度级别进行准确的蛋白质注释、跨物种蛋白质保守性分析以及语义推理。在本章的第一部分，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，我们提供一个关于PRO网站（proconsortium.org）的教程，用户可以在该网站浏览和搜索PRO层次结构、查看单个PRO术语的报告，并以层次表格视图、多序列比对视图和Cytoscape网络视图可视化PRO术语之间的关系。最后，我们描述几个示例，说明PRO中可用的独特而丰富的信息。
