Computational Metabolomics Operations at BioCyc.org
Computational Metabolomics Operations at BioCyc.org
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DOI：
10.3390/metabo5020291
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发表时间：
2015-06-01
期刊：
影响因子：
4.1
通讯作者：
Paley, Suzanne
中科院分区：
文献类型：
--
作者：
Karp, Peter D.;Billington, Richard;Paley, Suzanne
BioCyc.org是一个基因组和代谢途径门户网站，涵盖5500种生物，包括智人、拟南芥、酿酒酵母和大肠杆菌。这些特定生物的数据库经历了不同程度的管理。EcoCyc（大肠杆菌百科全书）数据库是最高度策划的;其内容来自27，000份出版物。BioCyc中的MetaCyc（代谢百科全书）数据库是一个“通用”代谢数据库，描述了生命所有领域的途径，反应，酶和代谢物。代谢途径为分析代谢组学数据提供了一个组织框架，BioCyc网站为代谢组学数据提供了计算操作，包括代谢物搜索和跨多个代谢物数据库的代谢物标识符的翻译。该网站允许研究人员使用一种名为SmartTables的设备存储和操作代谢物列表，该设备支持代谢物富集分析。该分析操作识别对于特定代谢途径的底物在统计学上过度代表的代谢物集合。BioCyc还可以在单个途径图和生物体特定的代谢图谱上可视化代谢组学数据，这些代谢图谱可用于每个BioCyc生物体。这些操作中的大多数既可以交互式地使用，也可以作为编程Web服务使用。
BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli. These organism-specific databases have undergone variable degrees of curation. The EcoCyc (Escherichia coli Encyclopedia) database is the most highly curated; its contents have been derived from 27,000 publications. The MetaCyc (Metabolic Encyclopedia) database within BioCyc is a "universal" metabolic database that describes pathways, reactions, enzymes and metabolites from all domains of life. Metabolic pathways provide an organizing framework for analyzing metabolomics data, and the BioCyc website provides computational operations for metabolomics data that include metabolite search and translation of metabolite identifiers across multiple metabolite databases. The site allows researchers to store and manipulate metabolite lists using a facility called SmartTables, which supports metabolite enrichment analysis. That analysis operation identifies metabolite sets that are statistically over-represented for the substrates of specific metabolic pathways. BioCyc also enables visualization of metabolomics data on individual pathway diagrams and on the organism-specific metabolic map diagrams that are available for every BioCyc organism. Most of these operations are available both interactively and as programmatic web services.