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One reason we are looking at ontology standards such as OWL is that we buy into the community who develop reasoning tools for these standards.

4Versa is a nice tool that operates at the Rdf level.  One nice side-effect is that since 'owl:Class' is an 'rdfs:SubClassOf' 'rdfs:Class' then we can use the 4Versa 'type' construct to find instances of OWL classes.  4Versa comes with some nice set operations.  It is well worth having a look through the documentation page which comes with the installation.  A pdf from version 4Suite 1.0b1 is "here.":files/Versa.pdf 

"Racer":http://www.sts.tu-harburg.de/~r.f.moeller/racer/ is a DL based reasoner, i.e. it operates in a domain of logic that OWL is based on, well that OWL-DL is based on, which is the subset of OWL that we are trying to adhere too.  Racer is used for classification and constraints checking in the OWL plugin for Protege.