When mapping ontologies you look for classes that are identical and can be directly mapped. Here with DBpedia, the classes Place, Organization and Person can be directly mapped to Location, Organization and Person in PROTON.
The rest of the classes do not have a direct equivalent in PROTON. Therefore you can sub-class them to the class of entities that is more general, in this case the protons:Entity:
Create a new file (e.g. dbpedia_proton.nt) into the dbpedia folder. There you put the mapping statements to sub-class the classes of the new ontology to their PROTON equivalents:
Finally add a record of this mapping file in the imports and defaultNS sections in KIM/config/owlim.ttl.
Now you have entities from both ontolgies (PROTON and DBpedia) in the semantic repository (OWLIM). But in order to properly use them for recognizing their mentions in texts, you need somehow to differentiate them.