title: The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
abstract: 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.
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Ron
authors.initials: R
authors.lastname: Caspi
authors.forename: Hartmut
authors.initials: H
authors.lastname: Foerster
authors.forename: Carol A
authors.initials: CA
authors.lastname: Fulcher
authors.forename: Pallavi
authors.initials: P
authors.lastname: Kaipa
authors.forename: Markus
authors.initials: M
authors.lastname: Krummenacker
authors.forename: Mario
authors.initials: M
authors.lastname: Latendresse
authors.forename: Suzanne
authors.initials: S
authors.lastname: Paley
authors.forename: Seung Y
authors.initials: SY
authors.lastname: Rhee
authors.forename: Alexander G
authors.initials: AG
authors.lastname: Shearer
authors.forename: Christophe
authors.initials: C
authors.lastname: Tissier
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Walk
authors.forename: Peifen
authors.initials: P
authors.lastname: Zhang
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
mesh_terms: D000818:Animals; D001105:Archaea / Q000201:enzymology / Q000235:genetics; D001419:Bacteria / Q000201:enzymology / Q000235:genetics; D019295:Computational Biology; D030541:Databases, Genetic; D004798:Enzymes / Q000378:metabolism*; D005658:Fungi / Q000201:enzymology / Q000235:genetics; D023281:Genomics; D020407:Internet; D053858:Metabolic Networks and Pathways / Q000235:genetics; D010944:Plants / Q000201:enzymology / Q000235:genetics; D012984:Software; D014584:User-Computer Interface
chemical_list: D004798:Enzymes