Using SyncReasoner to create an hierarchy

[alkidbaci]

Simplified problem:

Creating a ClassHierarchy, ObjectPropertyHierarchy or DatatypePropertyHierarchy using SyncReasoner will raise an error with the bottom entities (owl:Nothing, owl:bottomObjectProperty, owl:bottomDataProperty). The issue is related with the base class AbstractHierarchy, specifically the _init method. The problem happens because owlapi does not consider the bottom entities as entities in the signature but considers them as subentities. The setup fails when setting up transitive relations for bottom entities after trying to index them in the set of entities in signature.

Refer to issue 507 in Ontolearn for more details about the error.