Ontology should not redefine standard OWL and RDFS properties
There is no need to redefine the standard elements rdfs:comment, owl:deprecatedClass, owl:deprecatedProperty, owl:qualifiedCardinality - and in fact, the way it's done can cause problems in applications importing spdx along with other ontologies: specifically my company had a fairly hard to track down reasoning problem caused by the redefinition of rdfs:comment.
Further, OWL does not even have owl:deprecatedClass, owl:deprecatedProperty - it has the property owl:deprcated and the classes owl:DeprecatedClass, owl:DeprecatedProperty (notice capital D).
I don't believe there was an intent to redefine any of these terms. This is likely an error in the OWL file which include references to those terms.
@rivettp Could you create a pull request which corrects these errors for review?
Since resolving this would break some of the SPDX 2.X tooling, I'm moving this issue to 3.0.
This is now resolved with the 3.0 release - we've basically moved to SHACL for validation.