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.
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.
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.
|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|