Mapping between instances of the same ontology

[Edoardo Bianchi]

Dear experts,

I'm working on my PhD thesis and a problem has come up.
Using ProtegeOWL 3.4, I created an owl ontology that describes a
competency profile and I populated it with a few instances, at this
point I would like to make comparisons between the ontology instances (a
kind of mapping between instances of the same ontology) and extablish
some metric comparison.
What methods or tools do you recommend to use? I've heard good things
about the reasoner RACER and JRACER API.

Thank you very much
Edoardo Bianchi