This is why Lenat and CYC had settled on micro-theories. They found it impossible to build a useful universal ontology so had to fracture them on domain boundaries.
I'm somewhat familiar with Cyc but I'd never heard of this development of "micro-theories". It makes perfect sense though - to generalize hugely structured ontologies break as soon as the second person tries to use them or they are used on a slightly different domain.
Anyway, Prolog should be suitable for reasoning over them, but it is only grounded in the "micro-theory" part.
