Use of a transitive property in a property chain axiom is throwing a reasoner error

[dillerm]

If you run HermiT on ktao-merged.owl, it throws the following error: The given property hierarchy is not regular. There is a cyclic dependency involving property <http://purl.obolibrary.org/obo/BFO_0000050>.

Basically, OWL 2 DL places global restrictions on object properties to ensure that OWL 2 DL is decidable. One of these restrictions is that you are not allowed to use a transitive property, like part-of (BFO:0000050), in a property chain axiom, like in the example below:

<owl:propertyChainAxiom rdf:parseType="Collection"> 
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>  
        <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000063"/>  
</owl:propertyChainAxiom>

There seems to be quite a few more of these axioms, other than this one, in the ontology.