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Nucleic Acids Research, 2004, Vol. 32, Database issue D438-D442
© 2004 Oxford University Press

MetaCyc: a multiorganism database of metabolic pathways and enzymes

Cynthia J. Krieger, Peifen Zhang1, Lukas A. Mueller2, Alfred Wang, Suzanne Paley, Martha Arnaud, John Pick, Seung Y. Rhee1 and Peter D. Karp*

SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, 1 Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA and 2 Cornell University, Emerson Hall Room 251, Ithaca, NY 14853, USA

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

The MetaCyc database (see URL http://MetaCyc.org) is a collection of metabolic pathways and enzymes from a wide variety of organisms, primarily microorganisms and plants. The goal of MetaCyc is to contain a representative sample of each experimentally elucidated pathway, and thereby to catalog the universe of metabolism. MetaCyc also describes reactions, chemical compounds and genes. Many of the pathways and enzymes in MetaCyc contain extensive information, including comments and literature citations. SRI’s Pathway Tools software supports querying, visualization and curation of MetaCyc. With its wide breadth and depth of metabolic information, MetaCyc is a valuable resource for a variety of applications. MetaCyc is the reference database of pathways and enzymes that is used in conjunction with SRI’s metabolic pathway prediction program to create Pathway/Genome Databases that can be augmented with curation from the scientific literature and published on the world wide web. MetaCyc also serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research, education, metabolic engineering and systems biology. In the past 2 years the data content and the Pathway Tools software used to query, visualize and edit MetaCyc have been expanded significantly. These enhancements are described in this paper.


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