Caspi Ron, Billington Richard, Ferrer Luciana, Foerster Hartmut, Fulcher Carol A, Keseler Ingrid M, Kothari Anamika, Krummenacker Markus, Latendresse Mario, Mueller Lukas A, Ong Quang, Paley Suzanne, Subhraveti Pallavi, Weaver Daniel S, Karp Peter D
SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
FCEN, University of Buenos Aires and CONICET, Argentina.
Nucleic Acids Res. 2016 Jan 4;44(D1):D471-80. doi: 10.1093/nar/gkv1164. Epub 2015 Nov 2.
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.
MetaCyc数据库（MetaCyc.org）是一个可免费访问的综合性数据库，描述了来自生命所有领域的代谢途径和酶。MetaCyc中的大多数途径都是通过实验确定的小分子代谢途径。MetaCyc包含从超过46000篇出版物中获得的2400多条途径，是最大的经过整理的代谢途径集合。BioCyc（BioCyc.org）是一个包含5700个特定生物体的途径/基因组数据库（PGDB）的集合，每个数据库都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、转运系统和途径填补物。BioCyc网站提供了多种用于查询和分析PGDB的工具，包括组学查看器和比较分析工具。本文介绍了过去两年MetaCyc和BioCyc的新进展，包括添加化合物和反应的吉布斯自由能值；重新设计主要基因/蛋白质页面；添加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以及跨生物体搜索；以及代谢物标识符翻译服务。
