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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, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD

Nucleic Acids Res, vol. 40, no. D1, pp. D742-D753, 2012.


The MetaCyc database ( provides 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. MetaCyc contains more than 1800 pathways derived from more than 30‚ÄČ000 publications, and is the largest curated collection of metabolic pathways currently available. Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes and literature citations. BioCyc ( is a collection of more than 1700 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 database, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs contain additional features, including predicted operons, transport systems and pathway-hole fillers. The BioCyc website and Pathway Tools software offer many tools for querying and analysis of PGDBs, including Omics Viewers and comparative analysis. New developments include a zoomable web interface for diagrams; flux-balance analysis model generation from PGDBs; web services; and a new tool called Web Groups.

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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
Altman, Tomer Scientific Application Programmer
Caspi, Ron MetaCyc Curator
Dreher, Kate Database Curator
Fulcher, Carol A Scientific Database Curator
Karp, Peter D Director, Bioinformatics Research Group
Keseler, Ingrid M Senior Scientific Database Curator
Kothari, Anamika Scientific Datatabase Curator
Krummenacker, Markus Bioinformatics Scientist
Latendresse, Mario Computer Scientist
Ong, Quang Scientific Application Programmer
Paley, Suzanne Computer Scientist
Pujar, Anurahda Database Curator
Shearer, Alexander Biologist
Subhraveti, Pallavi Scientific Programmer
Travers, Mike Alumnus
Zhang, Peifen Database Curator

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