MetaCyc Overview

MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 1790 pathways from more than 2216 different organisms [more], and is curated from the scientific experimental literature. [more]

MetaCyc contains pathways involved in both primary [def] and secondary [def] metabolism, as well as associated compounds, enzymes, and genes. [more]

Motivations

The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. [MetaCyc mission]

MetaCyc is used in a variety of scientific applications, such as providing a reference data set for computationally predicting the metabolic pathways of organisms from their sequenced genomes, supporting metabolic engineering, helping to compare biochemical networks, and serving as an encyclopedia of metabolism. [scientific applications]

Recent Publication

• The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases, Nucleic Acids Research 40:D742-D753 2012.

Query and Visualization

MetaCyc pathways can be browsed from a list, from ontologies [def], or queried directly when searching for pathways, proteins, reactions or compounds. [more] MetaCyc can also be queried programmatically using Java or PERL when installed locally. [more]

New Users

Get a bird's eye view of the MetaCyc web site here.

How to Cite MetaCyc

Please cite MetaCyc as Caspi et al., 2012, "The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases", Nucleic Acids Research in publications resulting from its use.

Acknowledgments

The development of MetaCyc is funded by grant GM080746 from the NIH National Institute of General Medical Sciences and by grant DE-SC0004878 from the Department of Energy.