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Publication Details

MetaCyc: a multiorganism database of metabolic pathways and enzymes

by Krieger, C. J. and Zhang, P and Mueller, L. A. and Wang, A. and Paley, S. and Arnaud, M. and Pick, J. and Rhee, S. Y. and Karp, P. D.

Nucleic Acids Research, vol. 32, pp. D438-D442, 2004.

Abstract

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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Copyright ©2004 Oxford University Press

Associated Projects

MetaCyc

MetaCyc: Metabolic Pathway Database

MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1800 pathways from more than 2200 different organisms (circa 2012). The MetaCyc data were curated from more than 33,000 scientific publications. MetaCyc describes metabolic pathways, reactions, enzymes, and metabolites.

AIC Personnel

Name Title E-mail
Karp, Peter D Director, Bioinformatics Research Group
Paley, Suzanne Computer Scientist
Pick, John Alumnus

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