PRO: A Protein Ontology in Open Biomedical Ontologies

描述（由申请人提供）：生物医学本体在基因组和蛋白质组学研究中越来越重要，这些研究需要整合不同资源中的复杂数据。特别是，基因本体（GO）已经成为基因组注释的标准，开放生物医学本体（OBO）是跨生物医学领域共享的本体的保护伞。然而，目前的OBO库——蛋白质类及其关系的本体——存在一个缺口。该项目的目标是开发一个蛋白质本体（PRO），以促进蛋白质注释和功能发现。PRO将在OBO铸造厂内开发，采用在本体开发中指定最佳实践的原则。该项目的具体目标是：(i)开发一个蛋白质进化（ProEvo）本体，用于描述基于进化关系的蛋白质；（ii）开发一个蛋白质修饰形式（ProMod）本体，用于表示一个基因的多种蛋白质形式；（iii）指定PRO、GO和其他OBO本体之间的关系；（iv）传播PRO本体并开展科学案例研究。ProEvo将基于人工筛选的PIRSF和PANTHER全长蛋白家族及其在SCOP和Pfam中的组成结构域开发，最初用于人类含蛋白类。ProEvo类及其与GO术语的关系将形式化植物发育与功能之间的关系，从而基于实验证据对功能进行更一致和准确的推断。ProMod将定义由遗传变异、选择性剪接、蛋白水解裂解和翻译后修饰产生的蛋白质产物，最初是针对人类和小鼠蛋白质，使用UniProtKB/Swiss-Prot和小鼠基因组计划中完全整理的条目，以支持在精确水平上对蛋白质组进行变异、同工异构体和修饰产物的特定注释。基于人类和小鼠疾病蛋白的科学案例研究，PRO、GO和其他OBO本体（如疾病本体）之间的关系将捕获疾病理解所需的关系。对于PRO。向社区传播，将本体整合到OBO中，将新的关系添加到OBO关系本体中，并每年组织一次蛋白质本体研讨会。PRO也可以从PIR网站上获得，用于综合蛋白质分析。通过科学会议和合作，PRO联盟将与更广泛的科学界互动，以确保PRO有用并被广泛采用。PRO本体将允许研究人员探索蛋白质的功能和进化关系，以提高对疾病的理解，并确定潜在的诊断和治疗靶点。

DESCRIPTION (provided by applicant): Biomedical ontologies are increasingly important in genomic and proteomic research where complex data in disparate resources need to be integrated. In particular, the Gene Ontology (GO) has become a standard for genome annotation and the Open Biomedical Ontologies (OBO) is an umbrella for ontologies shared across biomedical domains. There is, however, a gap in the current OBO library-an ontology of protein classes and their relationships. The goal of the proposed project is to develop a PRotein Ontology (PRO) to facilitate protein annotation and functional discovery. PRO will be developed within the OBO Foundry, adopting principles specifying best practices in ontology development. The specific aims of this project are to: (i) develop a Protein Evolution (ProEvo) ontology for the description of proteins based on evolutionary relationships, (ii) develop an ontology for Protein Modified Forms (ProMod) for the representation of multiple protein forms of a gene, (iii) specify relationships between PRO, GO and other OBO ontologies, and (iv) disseminate PRO ontology and develop scientific case studies. ProEvo will be developed based on manually-curated families of full-length proteins in PIRSF and PANTHER and their constituent domains in SCOP and Pfam, initially for human protein-containing classes. The ProEvo classes and their relationships with GO terms will formalize the relationships between phytogeny and function, to allow more consistent and accurate inference of function based on experimental evidence. ProMod will define protein products generated by genetic variation, alternative splicing, proteolytic cleavage, and post-translational modification, initially for human and mouse proteins using fully-curated entries in UniProtKB/Swiss-Prot and the Mouse Genome Initiative, to support specific annotation of proteomes at the precise levels of variants, isoforms, and modified products. Defined based on scientific case studies of human and mouse disease proteins, the relations between PRO, GO, and other OBO ontologies, such as Disease Ontology, will capture the relationships required for disease understanding. For PRO .dissemination to the community, the ontology will be integrated into OBO, new relations will be added to the OBO Relations Ontology, and an annual protein ontology workshop will be organized. PRO will also be accessible from the PIR web site for integrative protein analysis. Through scientific meetings and collaborations, the PRO consortium will interact with the wider scientific community to ensure that PRO is useful and widely adopted. The PRO ontology will allow researchers to explore functional and evolutionary relationships of proteins to improve understanding of disease and identify potential diagnostic and therapeutic targets.