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I will also be hammering the relative advantage OWL has in this regard over RDF and RDFS, which both are so weak that no explanations are ever useful because no RDF/RDFS inferences are ever useful (Okay, a bit of an exaggeration, but still...)
Generally, I think identifying different data "facets" -- for lack of a better term -- and producing ontologies, or versions of an ontology, for each facet seems reasonable. It reminds me of the best practice from XML Land, where it's often said that a really complex apps needs several schemas.
The real trick is doing something clever in various reasoning systems to support this kind of faceted work.
Since Owlgres, in particular for us, is considerably less expressive but more scalable, one might build a more maximal ontology to check consistency but something more minimal (or none at all) to do query. Sure.
Ideally this process could be at least semi-automated; but I'm not familiar with any work in this area, though more well-informed folks might know otherwise.
Well another project for Bijan to start if that is the case :)