Publication Details

Using the MetaCyc pathway database and the BioCyc database collection

by Caspi R and Karp PD.

Curr Protoc Bioinformatics, vol. 20, pp. 1.17.1-1.17.51, 2007.

Abstract

The MetaCyc database (http://metacyc.org) is a collection of more than a thousand metabolic pathways from a wide variety of organisms, collected from the literature by manual curation. BioCyc contains more than 370 Pathway/Genome Databases, each of which describes the genome and predicted metabolic pathways of a single organism, as computationally predicted from the annotated genomes, using MetaCyc data as a reference. The protocols in this unit introduce the user to the extensive data content available in MetaCyc and BioCyc, and to mechanisms for querying, visualizing, and analyzing these data using the Pathway Tools software.

Electronic Copies

DOI 10.1002/0471250953.bi0117s20

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Associated Projects

	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: 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.

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