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How to merge two ontologies in Protege

I'm new to using Protege. I'm using two small owl files, both containing one super class and two sub classes. Both the ontologies are exactly same except for the class names. I imported both the files into a new file and merged one ontology to the other using refactor menu. I used "equivalent to" to map the corresponding classes of the ontologies and did the same for the properties. I want the SPARQL queries to fetch results from both the ontologies. How should I proceed?

There is an option Refactor->Merge ontologies , may be helpful?

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