Reference Databases

BiGG Database

The reference database file Ref BiGG.xls was reformatted from the data exported from BiGG.

The reference database file Ref BiGG GPR.xls was modified by adding Protein Index into the Ref BiGG.xls.

KEGG Database

The reference database file Ref KEGG.xls was reformatted from the data downloaded via KEGG'compound & KEGG's reaction.

MetaCyc database

The reference database file Ref MetaCyc.xls was reformatted from the data downloaded via MetaCyc.

Model SEED database

The reference database file Ref SEED.xls was reformatted from the data downloaded via Model SEED.

Those database files can be used as the reference database for metabolic network reconstructions in GEMSiRV.

Users can freely edit and update the reference database in GEMSiRV to the user-defined database and easily share with other users by exporting to a spreedsheet file (.xls).

Please note that we have automatically assign the reaction compartment in reference databases (KEGG, MetCyc and Model SEED) to cytoplasm unless otherwise specified.

Format of database

Layout of excel sheets as input for the reference database:

Metabolite Index:

Abbreviation, Name, Formula, Charge, Keggid, Casnumber, Compound_names, Note

e.g. glc-D, D-Glucose, C6H12O6,0, C00031, 50-99-7, alpha-D-Glucose/ beta-D-Glucose/ Grape sugar/ Dextrose/ Glucose, The content of metabolite "D-glucose" in the Ref BiGG.

Protein Index:

Abbreviation, Name, Note

e.g. Glk, Glucokinase, The content of protein "Glucokinase" in the Ref BiGG.

Reaction Index:

Abbreviation, Name, Equation, Keggid, Note

e.g. HEX1, hexokinase (D-glucose:ATP), [c] : atp + glc-D --> adp + g6p + h, R02848, The content of reaction "hexokinase (D-glucose:ATP)" in the Ref BiGG.

Cellular compartments

Reactions need to be assigned to specific cellular compartments [1].

Thylakoid is added as a new compartment [u].

[1] Reed, J.L., I. Famili, et al. (2006) "Towards multidimensional genome annotation.", Nature reviews, 7, 130-141.