I have a very simple class hierarchy, specified in OWL, with Protégé. For example:
-Person
--Man
--Woman
That is, every man is a person and every woman is a person.
When I include instances of Man and Woman, I expect that these instances would be included as instances of Person, as well. But the resulting classification is not as expected. Even when I run the reasoner.
I'm using owl 2 and Protégé 5.0.
Why Person is not including the instances of Man and Woman?
If you add Joel rdf:type Man, Joel will be a person. Double check your observation by using the DL query tab do get all instances of Person (I.e. Person is the query, make sure to check the necessary checkboxes on the right), or adding a view to your instance tab that is called inferred member list.
If all that does not work, try another reasoner (HermiT).