The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
by Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD
Nucleic Acids Res, vol. 40, no. D1, pp. D742-D753, 2012.
The MetaCyc database (http://metacyc.org/) provides a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains more than 1800 pathways derived from more than 30 000 publications, and is the largest curated collection of metabolic pathways currently available. Most reactions in MetaCyc pathways are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes and literature citations. BioCyc (http://biocyc.org/) is a collection of more than 1700 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference database, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs contain additional features, including predicted operons, transport systems and pathway-hole fillers. The BioCyc website and Pathway Tools software offer many tools for querying and analysis of PGDBs, including Omics Viewers and comparative analysis. New developments include a zoomable web interface for diagrams; flux-balance analysis model generation from PGDBs; web services; and a new tool called Web Groups.
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|
|Caspi, Ron||MetaCyc Curator|
|Dreher, Kate||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|
|Ong, Quang||Scientific Application Programmer|
|Paley, Suzanne||Computer Scientist|
|Pujar, Anurahda||Database Curator|
|Subhraveti, Pallavi||Scientific Programmer|
|Zhang, Peifen||Database Curator|