Reasoning with HermiT fails

[jamesaoverton]

Reasoning over the application ontology works on Protege 4.3.0 (build 304) with ELK 0.4.1, but with HermiT (1.3.8) it runs for 20 minutes then fails. I think it's getting stuck in some sort of loop and running out of memory.

Reasoning over ontofox.owl and ontorat.owl with HermiT works fine, so the problem is with uberon-module.owl. Uberon is developed using ELK. When I asked Chris Mungall last month he said that Uberon hasn't been tested with HermiT recently. So there could be a problem with our module or a problem with Uberon itself.

My preferred solution is something Chris suggested: an improved Extractor.java that uses a whitelist of just a few ObjectProperties. This will make the uberon-module.owl much smaller, and either fix the problem or help isolate the cause.