title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
abstract: The MetaCyc database (http://metacyc.org/) 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 30,000 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 (http://biocyc.org/) 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.
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA, USA.
authors.forename: Ron
authors.initials: R
authors.lastname: Caspi
authors.forename: Tomer
authors.initials: T
authors.lastname: Altman
authors.forename: Kate
authors.initials: K
authors.lastname: Dreher
authors.forename: Carol A
authors.initials: CA
authors.lastname: Fulcher
authors.forename: Pallavi
authors.initials: P
authors.lastname: Subhraveti
authors.forename: Ingrid M
authors.initials: IM
authors.lastname: Keseler
authors.forename: Anamika
authors.initials: A
authors.lastname: Kothari
authors.forename: Markus
authors.initials: M
authors.lastname: Krummenacker
authors.forename: Mario
authors.initials: M
authors.lastname: Latendresse
authors.forename: Lukas A
authors.initials: LA
authors.lastname: Mueller
authors.forename: Quang
authors.initials: Q
authors.lastname: Ong
authors.forename: Suzanne
authors.initials: S
authors.lastname: Paley
authors.forename: Anuradha
authors.initials: A
authors.lastname: Pujar
authors.forename: Alexander G
authors.initials: AG
authors.lastname: Shearer
authors.forename: Michael
authors.initials: M
authors.lastname: Travers
authors.forename: Deepika
authors.initials: D
authors.lastname: Weerasinghe
authors.forename: Peifen
authors.initials: P
authors.lastname: Zhang
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
mesh_terms: D016208:Databases, Factual; D004734:Energy Metabolism; D004798:Enzymes / Q000378:metabolism*; D016678:Genome; D023281:Genomics; D020407:Internet; D053858:Metabolic Networks and Pathways; D055432:Metabolomics; D012984:Software
chemical_list: D004798:Enzymes
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