Table 1

Overview of metabolic pathway databases used

Database

Export formats used

Versiona

Downloaded from


BiGG

Flat file, SBML

1

http://bigg.ucsd.edu/ webcite

EHMN

Excel

2

http://www.ehmn.bioinformatics.ed.ac.uk/ webcite

HumanCyc

Flat file

15.0

http://biocyc.org/download.shtml webcite

KEGG

Flat file, KGML

58

ftp://ftp.genome.jp/pub/kegg/ webcite

Reactome

MySQL database

36

http://reactome.org/download/index.html webcite


aDownloaded in the first week of May 2011

KGML: KEGG Markup Language; SBML: Systems Biology Markup Language.

Stobbe et al. BMC Systems Biology 2011 5:165   doi:10.1186/1752-0509-5-165

Open Data