title: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.
abstract: The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. The majority of MetaCyc pathways are small-molecule metabolic pathways that have been experimentally determined. MetaCyc contains more than 2400 pathways derived from >46,000 publications, and is the largest curated collection of metabolic pathways. BioCyc (BioCyc.org) is a collection of 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems, and pathway-hole fillers. The BioCyc website offers a variety of tools for querying and analyzing PGDBs, including Omics Viewers and tools for comparative analysis. This article provides an update of new developments in MetaCyc and BioCyc during the last two years, including addition of Gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; several new search capabilities, including searching for genes based on sequence patterns, searching for databases based on an organism's phenotypes, and a cross-organism search; and a metabolite identifier translation service.
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Ron
authors.initials: R
authors.lastname: Caspi
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Billington
authors.affiliation: FCEN, University of Buenos Aires and CONICET, Argentina.
authors.forename: Luciana
authors.initials: L
authors.lastname: Ferrer
authors.affiliation: Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA.
authors.forename: Hartmut
authors.initials: H
authors.lastname: Foerster
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Carol A
authors.initials: CA
authors.lastname: Fulcher
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Ingrid M
authors.initials: IM
authors.lastname: Keseler
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Anamika
authors.initials: A
authors.lastname: Kothari
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Markus
authors.initials: M
authors.lastname: Krummenacker
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Mario
authors.initials: M
authors.lastname: Latendresse
authors.affiliation: Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA.
authors.forename: Lukas A
authors.initials: LA
authors.lastname: Mueller
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Quang
authors.initials: Q
authors.lastname: Ong
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Paley
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Pallavi
authors.initials: P
authors.lastname: Subhraveti
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Weaver
authors.affiliation: SRI International, 333 Ravenswood, Menlo Park, CA 94025, USA pkarp@ai.sri.com.
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
mesh_terms: D062126:Databases, Chemical; D030541:Databases, Genetic; D004579:Electron Transport; D004798:Enzymes / Q000378:metabolism*; D016678:Genome; D020407:Internet; D053858:Metabolic Networks and Pathways / Q000235:genetics; D012984:Software
chemical_list: D004798:Enzymes