Before revision:  Vertices may represent either chemical substances, or reactions , or both . A common practice in the analysis of metabolic networks is to preprocess the network by deleting so called currency metabolites -- abundant molecular species that react with a large number of metabolites. One of several reasons to do this is that they do not put any constraint on the reactions, and thus do not give much information of the higher order functionality of the system.
After revision:  Vertices may represent either chemical substances, or reactions , or both ? Should vertices represent substances or reactions? Different definitions encode different information about the reaction system.