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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, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD.

Nucleic Acids Res., vol. 42, no. 1, pp. D459-D471, 2014.

Abstract

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains >2100 pathways derived from >37 000 publications, and is the largest curated collection of metabolic pathways currently available. BioCyc (BioCyc.org) is a collection of >3000 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. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome Project. The BioCyc Web site offers a variety of tools for querying and analysis of PGDBs, including Omics Viewers and tools for comparative analysis. New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.

Electronic Copies

DOI
10.1093/nar/gkt1103

Adobe PDF

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 1800 pathways from more than 2200 different organisms (circa 2012). The MetaCyc data were curated from more than 33,000 scientific publications. MetaCyc describes metabolic pathways, reactions, enzymes, and metabolites.

AIC Personnel

Name Title E-mail
Altman, Tomer Scientific Application Programmer
Billington, Richard Senior Software Engineer
Brito, Deepika Scientific Database Curator
Caspi, Ron MetaCyc Curator
Dreher, Kate Database Curator
Foester, Hartmut Database Curator
Fulcher, Carol A Scientific Database Curator
Holland, Tim Software Engineer
Karp, Peter D Director, Bioinformatics Research Group
Keseler, Ingrid M Senior Scientific Database Curator
Kothari, Anamika Scientific Datatabase Curator
Krummenacker, Markus Bioinformatics Scientist
Kubo, Aya Scientific Database Curator
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
Zhang, Peifen Database Curator

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