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.

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.