The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
by Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Paley S, Popescu L, Pujar A, Shearer AG, Zhang P, Karp PD
Nucleic Acids Res, vol. 38, pp. D473-D479, 2010.
The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism.
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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. |
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Altman, Tomer | Scientific Application Programmer |  |
| Caspi, Ron | Scientific Database Curator | |
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| Fulcher, Carol A | Scientific Database Curator | |
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| Gilham, Fred | Software Engineer | ||
| 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 | |
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| Subhraveti, Pallavi | Scientific Programmer | |
