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Nucleic Acids Research Advance Access published online on October 27, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm900
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

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

Ron Caspi1, Hartmut Foerster2, Carol A. Fulcher1, Pallavi Kaipa1, Markus Krummenacker1, Mario Latendresse1, Suzanne Paley1, Seung Y. Rhee2, Alexander G. Shearer1, Christophe Tissier2, Thomas C. Walk2, Peifen Zhang2 and Peter D. Karp1,*

1SRI International, 333 Ravenswood, Menlo Park, CA 94025 and 2Department of Plant Biology, Carnegie Institution, 260 Panama Street, Stanford, CA 94305, USA

*To whom correspondence should be addressed. Tel: +1 650 859 4358; Fax: +1 650 859 3735; Email: pkarp{at}ai.sri.com

Received September 12, 2007. Accepted October 4, 2007.

MetaCyc (MetaCyc.org) is a universal database of metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are curated from the primary scientific literature, and are experimentally determined small-molecule metabolic pathways. Each reaction in a MetaCyc pathway is annotated with one or more well-characterized enzymes. Because MetaCyc contains only experimentally elucidated knowledge, it provides a uniquely high-quality resource for metabolic pathways and enzymes. BioCyc (BioCyc.org) is a collection of more than 350 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the predicted metabolic network of one organism, including metabolic pathways, enzymes, metabolites and reactions predicted by the Pathway Tools software using MetaCyc as a reference database. BioCyc PGDBs also contain predicted operons and predicted pathway hole fillers—predictions of which enzymes may catalyze pathway reactions that have not been assigned to an enzyme. The BioCyc website offers many tools for computational analysis of PGDBs, including comparative analysis and analysis of omics data in a pathway context. The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism.

The authors wish it to be known that, in their opinion, the first 13 authors should be regarded as joint First Authors.


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