I think that GO with GO-CAM is definitely going that way. Basic GO is rather simple and can't infer that much (as in GO by itself has low classification or inference logic build in). Uberon, for anatomy, does use a lot of OWL power and shows that the logic-based inference can help a lot.
Reactome, is a graph, because that is the domain. But technically it does little with that fact (In my disappointed opinion).
Given that GO and Reactome are also relatively small academic efforts in general...