The UniProt Knowledgebase UniProtKB is a comprehensive, high-quality, and freely accessible resource of protein sequences and functional annotation that covers genomes and proteomes from tens of thousands of taxa, including a broad range of plants and microorganisms producing natural products of medical, nutritional, and agronomical interest. Here we describe work that enhances the utility of UniProtKB as a support for both the study of natural products and for their discovery. The foundation of this work is an improved representation of natural product metabolism in UniProtKB using Rhea, an expert-curated knowledgebase of biochemical reactions, that is built on the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Knowledge of natural products and precursors is captured in ChEBI, enzyme-catalyzed reactions in Rhea, and enzymes in UniProtKB/Swiss-Prot, thereby linking chemical structure data directly to protein knowledge. We provide a practical demonstration of how users can search UniProtKB for protein knowledge relevant to natural products through interactive or programmatic queries using metabolite names and synonyms, chemical identifiers, chemical classes, and chemical structures and show how to federate UniProtKB with other data and knowledge resources and tools using semantic web technologies such as RDF and SPARQL. All UniProtKB data are freely available for download in a broad range of formats for users to further mine or exploit as an annotation source, to enrich other natural product datasets and databases.

中文翻译：

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不同化学物质的不同分类法：UniProtKB 中天然产物代谢的增强表示


UniProt 知识库 UniProtKB 是一个全面、高质量且可免费访问的蛋白质序列和功能注释资源，涵盖数以万计的分类群的基因组和蛋白质组，包括生产医疗、营养、和农艺兴趣。在这里，我们描述了增强 UniProtKB 实用性的工作，以支持天然产物的研究和发现。这项工作的基础是使用 Rhea 改进 UniProtKB 中天然产物代谢的表示，Rhea 是专家策划的生化反应知识库，建立在小分子 ChEBI（生物兴趣化学实体）本体之上。 ChEBI 捕获天然产物和前体的知识，Rhea 捕获酶催化反应，UniProtKB/Swiss-Prot 捕获酶，从而将化学结构数据直接与蛋白质知识联系起来。我们提供了一个实际演示，说明用户如何使用代谢物名称和同义词、化学标识符、化学类别和化学结构，通过交互式或编程查询在 UniProtKB 中搜索与天然产物相关的蛋白质知识，并展示如何将 UniProtKB 与其他数据和知识资源联合以及使用 RDF 和 SPARQL 等语义 Web 技术的工具。所有 UniProtKB 数据都可以多种格式免费下载，供用户进一步挖掘或利用作为注释源，以丰富其他天然产物数据集和数据库。