PRO: A Protein Ontology in Open Biomedical Ontologies

PRO：开放生物医学本体中的蛋白质本体

• 批准号: 7255227
• 负责人: CATHY H. WU
• 金额: $ 53.93万
• 依托单位: GEORGETOWN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-05-01 至 2011-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7255227
• 关键词: Abbreviations; Adopted; Alternative Splicing; Animal Model; Base Sequence; Binding; Biogenesis; Biological; Biological Process; Case Study; Categories; Cereals; Class; Classification; Cleaved cell; Collaborations; Communities; Complex; Controlled Vocabulary; Data; Databases; Deposition; Development; Diagnostic; Disease; Educational workshop; Ensure; Event; Evolution; Family; Genes; Genetic; Genetic Variation; Genome; Genomics; Goals; Human; Human Biology; Individual; Informatics; Internet; Laboratories; Length; Libraries; Location; Modeling; Modification; Molecular; Mouse Protein; Mus; Mutation; Names; Nomenclature; Ontology; Organelles; Pathway interactions; Pattern; Plant Roots; Post-Translational Protein Processing; Principal Investigator; Process; Property; Protein Analysis; Protein Databases; Protein Family; Protein Isoforms; Protein Structure Initiative; Proteins; Proteome; Proteomics; RNA Splicing; Research; Research Personnel; Resources; Role; Site; Source; Specific qualifier value; Standards of Weights and Measures; Structure; SwissProt; System; Tertiary Protein Structure; Testing; Text; Training; Transcript; Translations; Unified Medical Language System; Validation; Variant; Visual; Work; base; data integration; disease phenotype; genetic variant; graphical user interface; improved; interoperability; model organisms databases; mouse genome; programs; therapeutic target; tool

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.

描述（由申请人提供）：生物医学本体在基因组和蛋白质组研究中变得越来越重要，在这些研究中需要整合不同资源中的复杂数据。特别是，基因本体（GO）已成为基因组注释的标准，而开放生物医学本体（OBO）是跨生物医学领域共享本体的保护伞。然而，当前的 OBO 库存在一个空白——蛋白质类别及其关系的本体论。该项目的目标是开发蛋白质本体论（PRO）以促进蛋白质注释和功能发现。 PRO 将在 OBO Foundry 内开发，采用指定本体开发最佳实践的原则。该项目的具体目标是：（i）开发蛋白质进化（ProEvo）本体，用于基于进化关系描述蛋白质，（ii）开发蛋白质修饰形式（ProMod）本体，用于表示多种蛋白质形式(iii) 明确 PRO、GO 和其他 OBO 本体之间的关系，以及 (iv) 传播 PRO 本体并开展科学案例研究。 ProEvo 将基于 PIRSF 和 PANTHER 中手动策划的全长蛋白质家族及其 SCOP 和 Pfam 中的组成域进行开发，最初用于包含人类蛋白质的类别。 ProEvo 类别及其与 GO 术语的关系将形式化植物发生和功能之间的关系，以便根据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、蛋白水解切割和翻译后修饰产生的蛋白质产物，最初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策划的条目，以支持特定注释精确水平的变体、亚型和修饰产物的蛋白质组。 PRO、GO 和其他 OBO 本体（例如疾病本体）之间的关系是根据人类和小鼠疾病蛋白的科学案例研究定义的，将捕获疾病理解所需的关系。为了向社区传播PRO，本体将被整合到OBO中，新的关系将被添加到OBO关系本体中，并且将组织年度蛋白质本体研讨会。还可以从 PIR 网站访问 PRO 进行综合蛋白质分析。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 有用并得到广泛采用。 PRO本体将使研究人员能够探索蛋白质的功能和进化关系，以增进对疾病的理解并确定潜在的诊断和治疗靶点。