29. The computer-implemented method of claim 28 further comprising generating a refined simplified ontology and wherein applying the query comprises applying the query to the refined simplified ontology to identify an instance of the query in said refined simplified ontology.
29. The computer-implemented method of claim 28 further comprising generating a refined simplified ontology and wherein applying the query comprises applying the query to the refined simplified ontology to identify an instance of the query in said refined simplified ontology. 31. The computer-implemented method of claim 29 wherein applying at least one transformation comprises performing at least one of: simplifying relationships in the original ontology, comprising inserting at least one new relationship; collapsing individuals in the original ontology, comprising adding at least one new individual to encompass more than one individual from the original ontology; and eliminating concepts in the original ontology, comprising inserting at least one new concept.