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Well, so we have the same use case.
As already answered by JiBa, you may use the default_world object or some specific one if you defined one to access the entities. I found it convenient to use SPARQL queries at times to perform such operations, otherwise you might just navigate the classes following the specific properties defined in your ontology(ies).
I am not sure about the reasoner from within owlready as I did not use it extensively. My few attempts seem to demonstrate it did make use of all imported assertions, not only these of the top ontology though.
Hope this helps,
GP
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