The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

被引：592

作者：

Caspi, Ron ^{[1
]}

Altman, Tomer ^{[1
]}

Billington, Richard ^{[1
]}

Dreher, Kate ^{[2
]}

Foerster, Hartmut ^{[3
]}

Fulcher, Carol A. ^{[1
]}

Holland, Timothy A. ^{[1
]}

Keseler, Ingrid M. ^{[1
]}

Kothari, Anamika ^{[1
]}

Kubo, Aya ^{[1
]}

Krummenacker, Markus ^{[1
]}

Latendresse, Mario ^{[1
]}

Mueller, Lukas A. ^{[3
]}

Ong, Quang ^{[1
]}

Paley, Suzanne ^{[1
]}

Subhraveti, Pallavi ^{[1
]}

Weaver, Daniel S. ^{[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 | 2014年 / 42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：

SYSTEMS BIOLOGY; SOIL BACTERIUM; RNA-SEQ; GENOME; RECONSTRUCTION; MODEL; REVEALS; NETWORK; STRAIN; TOOLS;

D O I：

10.1093/nar/gkt1103

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 database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains >2100 pathways derived from >37 000 publications, and is the largest curated collection of metabolic pathways currently available. BioCyc (BioCyc.org) is a collection of >3000 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. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome Project. The BioCyc Web site offers a variety of tools for querying and analysis of PGDBs, including Omics Viewers and tools for comparative analysis. New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.

引用

页码：D459 / D471

页数：13

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