The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
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DOI：
10.1093/nar/gkv1164
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Karp PD
中科院分区：
文献类型：
--
作者：
Caspi R;Billington R;Ferrer L;Foerster H;Fulcher CA;Keseler IM;Kothari A;Krummenacker M;Latendresse M;Mueller LA;Ong Q;Paley S;Subhraveti P;Weaver DS;Karp PD
MetaCyc数据库（MetaCyc.org）是一个免费访问的综合数据库，描述了生命所有领域的代谢途径和酶。大多数MetaCyc途径是已经通过实验确定的小分子代谢途径。MetaCyc包含来自超过46，000篇出版物的2，400多种代谢途径，是最大的代谢途径精选集。BioCyc（BioCyc.org）是5700个生物体特异性途径/基因组数据库（PGDB）的集合，每个数据库包含一个生物体的完整基因组和预测的代谢网络，包括代谢物、酶、反应、代谢途径、预测的操纵子、运输系统和途径孔填充物。BioCyc网站提供了各种查询和分析PGDB的工具，包括组学查看器和比较分析工具。本文介绍了近两年来MetaCyc和BioCyc的最新进展，包括增加化合物和反应的吉布斯自由能值，重新设计基因/蛋白质主页，增加了一个用于创建包含多个链接途径的图表的工具，增加了一个用于创建包含多个链接途径的图表的工具，增加了一个用于创建包含多个链接途径的图表的工具。几种新的搜索功能，包括基于序列模式搜索基因，基于生物体表型搜索数据库，和跨生物体搜索;以及代谢物标识符翻译服务。
The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. The majority of MetaCyc pathways are small-molecule metabolic pathways that have been experimentally determined. MetaCyc contains more than 2400 pathways derived from >46 000 publications, and is the largest curated collection of metabolic pathways. BioCyc (BioCyc.org) is a collection of 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems, and pathway-hole fillers. The BioCyc website offers a variety of tools for querying and analyzing PGDBs, including Omics Viewers and tools for comparative analysis. This article provides an update of new developments in MetaCyc and BioCyc during the last two years, including addition of Gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; several new search capabilities, including searching for genes based on sequence patterns, searching for databases based on an organism's phenotypes, and a cross-organism search; and a metabolite identifier translation service.