The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

被引：809

作者：

Caspi, Ron ^{[1
]}

Billington, Richard ^{[1
]}

Ferrer, Luciana ^{[2
,3
]}

Foerster, Hartmut ^{[4
]}

Fulcher, Carol A. ^{[1
]}

Keseler, Ingrid M. ^{[1
]}

Kothari, Anamika ^{[1
]}

Krummenacker, Markus ^{[1
]}

Latendresse, Mario ^{[1
]}

Mueller, Lukas A. ^{[4
]}

Ong, Quang ^{[1
]}

Paley, Suzanne ^{[1
]}

Subhraveti, Pallavi ^{[1
]}

Weaver, Daniel S. ^{[1
]}

Karp, Peter D. ^{[1
]}

机构：

[1] SRI Int, 333 Ravenswood Ave, Menlo Pk, CA 94025 USA

[2] Univ Buenos Aires, FCEN, RA-1053 Buenos Aires, DF, Argentina

[3] Consejo Nacl Invest Cient & Tecn, RA-1033 Buenos Aires, DF, Argentina

[4] Cornell Univ, Boyce Thompson Inst Plant Res, Tower Rd, Ithaca, NY 14853 USA

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / D1期

基金：

美国国家卫生研究院;

关键词：

INFORMATION;

D O I：

10.1093/nar/gkv1164

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：D471 / D480

页数：10

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