A system for ontology candidate selection and comparison including a microprocessor and an ontology candidate selection component executing on the microprocessor and configured to compare at least a portion of a plurality of ontology candidates based on a candidate selection rule, and based on said comparison, select from the plurality of ontology candidates a pair of ontologies. The system further includes an ontology similarity component coupled to the ontology candidate selection component and configured to generate a similarity outcome related to the pair of ontologies based on a similarity rule and evaluate at least one of: the candidate selection rule or the similarity rule based on the similarity outcome.