I have a set of ontologies for which I use the Pellet reasoner to reason over in Protege 5.5.0. The reasoner completes inference over the ontologies in 20 seconds.
When I use the OWL API code implementation, it takes the Pellet reasoner 45 minutes to reason over the set of ontologies.
Where or how can I find the configuration settings used in the Protege Plugin, to compare it to the defaults for the OWL API implementation, which are currently being used?
I have tried to locate configurations in files in the installation, as well as in the source code for the Protege plu-gin, but I cannot figure out how it is configured.