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Publication Details

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

by Caspi R, Foerster H, Fulcher C. A, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee S. Y, Shearer A. G, Tissier C, Walk T. C, Zhang P, Karp P. D.

Nucleic Acids Research, vol. 36, pp. D623-D631, 2007.


MetaCyc ( 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 ( 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.

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BioCyc Database Collection

The BioCyc Database Collection is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism.


MetaCyc: Metabolic Pathway Database

MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 2500 pathways from more than 2800 different organisms (circa 2012). The MetaCyc data were curated from more than 50,000 scientific publications. MetaCyc describes metabolic pathways, reactions, enzymes, and metabolites.

AIC Personnel

Name Title E-mail
Caspi, Ron MetaCyc Curator
Fulcher, Carol A Scientific Database Curator
Karp, Peter D Director, Bioinformatics Research Group
Krummenacker, Markus Bioinformatics Scientist
Latendresse, Mario Computer Scientist
Paley, Suzanne Computer Scientist
Shearer, Alexander Biologist
Subhraveti, Pallavi Scientific Programmer

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