Before revision:  We find that a "substance network," where all metabolites participating in a reaction are connected, is a good trade-off between high functional overlap (between network modules and observed functions ) and a reasonable number of currency metabolites.
After revision:  We find that a "substance network," where all metabolites participating in a reaction are connected, is relatively better than others, evaluated both with respect to the functional overlap between modules and functions and to the number and identity of identified currency metabolites.