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

被引：435

作者：

Caspi, Ron ^{[1
]}

Altman, Tomer ^{[1
]}

Dreher, Kate ^{[2
]}

Fulcher, Carol A. ^{[1
]}

Subhraveti, Pallavi ^{[1
]}

Keseler, Ingrid M. ^{[1
]}

Kothari, Anamika ^{[1
]}

Krummenacker, Markus ^{[1
]}

Latendresse, Mario ^{[1
]}

Mueller, Lukas A. ^{[3
]}

Ong, Quang ^{[1
]}

Paley, Suzanne ^{[1
]}

Pujar, Anuradha ^{[3
]}

Shearer, Alexander G. ^{[1
]}

Travers, Michael ^{[1
]}

Weerasinghe, Deepika ^{[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 | 2012年 / 40卷 / D1期

基金：

美国国家科学基金会; 美国国家卫生研究院;

关键词：

GENOMICS; RECONSTRUCTION; TRANSCRIPTOME; CEREVISIAE; TOLERANCE; IDENTIFY; TOOLS; GENE;

D O I：

10.1093/nar/gkr1014

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 (http://metacyc.org/) provides 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. MetaCyc contains more than 1800 pathways derived from more than 30 000 publications, and is the largest curated collection of metabolic pathways currently available. Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes and literature citations. BioCyc (http://biocyc.org/) is a collection of more than 1700 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 database, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs contain additional features, including predicted operons, transport systems and pathway-hole fillers. The BioCyc website and Pathway Tools software offer many tools for querying and analysis of PGDBs, including Omics Viewers and comparative analysis. New developments include a zoomable web interface for diagrams; flux-balance analysis model generation from PGDBs; web services; and a new tool called Web Groups.

引用

页码：D742 / D753

页数：12

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