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 (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.
| DOI 10.1093/nar/gkm900 |
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BioCyc Database CollectionThe 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, with the exception of the MetaCyc database, which is a reference source on metabolic pathways from hundreds of organisms. |
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MetaCyc: Metabolic Pathway DatabaseThe MetaCyc metabolic pathway database contains pathways from over 150 different organisms. MetaCyc describes metabolic pathways, reactions, enzymes, and substrate compounds. The MetaCyc data were gathered from a variety of literature and on-line sources, and contain citations to the source of each pathway. |
| Name | Title | ||
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| Caspi, Ron | Scientific Database Curator |  |
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| Fulcher, Carol A | Scientific Database Curator | |
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| Kaipa, Pallavi | Scientific Programmer | |
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| Karp, Peter D | Director, Bioinformatics Research Group | |
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Krummenacker, Markus | Bioinformatics Scientist | |
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Latendresse, Mario | Computer Scientist | |
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Paley, Suzanne | Computer Scientist | |
| Shearer, Alexander | Biologist | |
