As far as I know, all ontologies are distributed without inferrence (= asserted only) and most tools (including Protégé) do not permit to save inferrences (however, Owlready can do that). So you can assume that your ontologies are asserted-only.
After loading the desired ontology(ies), you use the sync_reasoner() function for performing reasoning.
By default, Owlready places all inferred facts in a special ontology, named "http://inferrences/
". Consequently, they are not saved when you save the ontology in an RDF/XML file.
However, you can place the inferred facts in the ontology of your choice, as follows:
Using this syntax, all facts inferred by Hermit will be asserted in the given ontology.
See the doc for more details : http://owlready2.readthedocs.io/en/latest/reasoning.html