The order of the data integration for MetNetDB, with respect to Arabidopsis: AraCyc is the backbone of the whole database, then AGRIS is used to extend the networks. Other databases are integrated without any special order requirement. External data usually does not need any special transformation because the data can be easily added into to the database as a new field/label of a gene, a protein or a molecule. So the data integration from the external data source to MetNetDB is straightforward in most cases.
Sucaet et al. BMC Bioinformatics 2012 13:267 doi:10.1186/1471-2105-13-267