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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, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Karp PD.

Nucleic Acids Res, vol. 44, no. D1, pp. D471-D480, 2016.

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.

Electronic Copies

DOI
10.1093/nar/gkv1164

BibTeX

EndNote

Associated Projects

BioCyc

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

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
Billington, Richard Senior Software Engineer
Caspi, Ron MetaCyc Curator
Ferrer, Luciana Alumni
Foester, Hartmut 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
Mueller, Lukas Database Curator
Ong, Quang Scientific Application Programmer
Paley, Suzanne Computer Scientist
Subhraveti, Pallavi Scientific Programmer
Weaver, Daniel Systems Biologist

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