Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB.
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB.
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DOI：
10.3390/metabo11010048
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发表时间：
2021-01-12
期刊：
影响因子：
4.1
通讯作者：
On Behalf Of The UniProt Consortium
中科院分区：
文献类型：
--
作者：
Feuermann M;Boutet E;Morgat A;Axelsen KB;Bansal P;Bolleman J;de Castro E;Coudert E;Gasteiger E;Géhant S;Lieberherr D;Lombardot T;Neto TB;Pedruzzi I;Poux S;Pozzato M;Redaschi N;Bridge A;On Behalf Of The UniProt Consortium
UniProtKB是一个全面的、高质量的、免费获取的蛋白质序列和功能注释资源，涵盖了成千上万个分类群的基因组和蛋白质组，包括产生医学、营养和农学兴趣的天然产物的广泛的植物和微生物。在这里，我们描述了提高UniProtKB作为天然产物研究和发现的支持的效用的工作。这项工作的基础是使用Rhea改进了UniProtKB中天然产物代谢的表示，Rhea是一个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）本体上。天然产物和前体的知识在ChEBI、Rhea酶催化反应和UniProtKB/Swiss-Prot酶中被捕获，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的演示，说明用户如何通过使用代谢物名称和同义词、化学标识符、化学类和化学结构的交互式或程序化查询来搜索与天然产物相关的蛋白质知识，并展示了如何使用RDF和SPARQL等语义web技术将UniProtKB与其他数据和知识资源以及工具联合起来。所有的UniProtKB数据都以多种格式免费提供下载，供用户进一步挖掘或利用作为注释源，以丰富其他天然产品数据集和数据库。
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.
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影响因子：
14.9
作者：
Blum M;Chang HY;Chuguransky S;Grego T;Kandasaamy S;Mitchell A;Nuka G;Paysan-Lafosse T;Qureshi M;Raj S;Richardson L;Salazar GA;Williams L;Bork P;Bridge A;Gough J;Haft DH;Letunic I;Marchler-Bauer A;Mi H;Natale DA;Necci M;Orengo CA;Pandurangan AP;Rivoire C;Sigrist CJA;Sillitoe I;Thanki N;Thomas PD;Tosatto SCE;Wu CH;Bateman A;Finn RD
通讯作者：
Finn RD
影响因子：
14.9
作者：
Kanehisa M;Furumichi M;Sato Y;Ishiguro-Watanabe M;Tanabe M
通讯作者：
Tanabe M
影响因子：
14.9
作者：
The Gene Ontology Consortium
通讯作者：
The Gene Ontology Consortium
影响因子：
9.2
作者：
Bolleman, Jerven;de Castro, Edouard;Bridge, Alan
通讯作者：
Bridge, Alan
影响因子：
14.9
作者：
Altenhoff AM;Train CM;Gilbert KJ;Mediratta I;Mendes de Farias T;Moi D;Nevers Y;Radoykova HS;Rossier V;Warwick Vesztrocy A;Glover NM;Dessimoz C
通讯作者：
Dessimoz C