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.
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.
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 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.
|Billington, Richard||Senior Software Engineer|
|Caspi, Ron||MetaCyc Curator|
|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|