Figure 4
From: Path2Models: large-scale generation of computational models from biochemical pathway maps
Workflow indicating the SuBliMinaL Toolbox modules that were linked to produce draft metabolic models from the source data. KEGG extract and MetaCyc extract produce MIRIAM-annotated SBML representations of the contents of KEGG and MetaCyc, respectively. Metabolite and reaction ids are reconciled through reference to the MNXref namespace, unifying the metabolites to an assumed intracellular pH of 7.3, and mass and charge balancing reactions where possible. The Merge module merges the individual reconstructions from KEGG and MetaCyc, to which a limited growth medium and transport reactions are added, along with gene-protein relationships (GPRs) and flux bounds. The models are then formatted to allow for their analysis with the COBRA Toolbox and then released as draft models that represent the union of the information held in both KEGG and MetaCyc.