A survey of metabolic databases emphasizing the MetaCyc family.

Abstract:

:Thanks to the confluence of genome sequencing and bioinformatics, the number of metabolic databases has expanded from a handful in the mid-1990s to several thousand today. These databases lie within distinct families that have common ancestry and common attributes. The main families are the MetaCyc, KEGG, Reactome, Model SEED, and BiGG families. We survey these database families, as well as important individual metabolic databases, including multiple human metabolic databases. The MetaCyc family is described in particular detail. It contains well over 1,000 databases, including highly curated databases for Escherichia coli, Saccharomyces cerevisiae, Mus musculus, and Arabidopsis thaliana. These databases are available through a number of web sites that offer a range of software tools for querying and visualizing metabolic networks. These web sites also provide multiple tools for analysis of gene expression and metabolomics data, including visualization of those datasets on metabolic network diagrams and over-representation analysis of gene sets and metabolite sets.

journal_name

Arch Toxicol

journal_title

Archives of toxicology

authors

Karp PD,Caspi R

doi

10.1007/s00204-011-0705-2

subject

Has Abstract

pub_date

2011-09-01 00:00:00

pages

1015-33

issue

9

eissn

0340-5761

issn

1432-0738

journal_volume

85

pub_type

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