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

被引：329

作者：

Caspi, Ron ^{[1
]}

Altman, Tomer ^{[1
]}

Dale, Joseph M. ^{[1
]}

Dreher, Kate ^{[2
]}

Fulcher, Carol A. ^{[1
]}

Gilham, Fred ^{[1
]}

Kaipa, Pallavi ^{[1
]}

Karthikeyan, Athikkattuvalasu S. ^{[2
]}

Kothari, Anamika ^{[1
]}

Krummenacker, Markus ^{[1
]}

Latendresse, Mario ^{[1
]}

Mueller, Lukas A. ^{[3
]}

Paley, Suzanne ^{[1
]}

Popescu, Liviu ^{[1
]}

Pujar, Anuradha ^{[3
]}

Shearer, Alexander G. ^{[1
]}

Zhang, Peifen ^{[2
]}

Karp, Peter D. ^{[1
]}

机构：

[1] SRI Int, Menlo Pk, CA 94025 USA

[2] Carnegie Inst, Dept Plant Biol, Stanford, CA 94305 USA

[3] Cornell Univ, Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA

来源：

NUCLEIC ACIDS RESEARCH | 2010年 / 38卷

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

RECONSTRUCTION; SYSTEM;

D O I：

10.1093/nar/gkp875

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 comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism.

引用

页码：D473 / D479

页数：7

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