I used protege to create two ontology and I save as A.owl, B.owl. I know that the protege-4.0 can merge many ontology. I want to use protege-owl API to merge ontology A.owl
First load both A and B.
Then go to "Refactor > Merge Ontologies" from the menu.
Assume that you have opened A.owl in Protege. Go to the "Active Ontology" tab. Click on the plus sign beside the Direct Imports text. Click on the button for "Direct Imports" and import "B.owl". Then go to "Refactor" > "Merge Ontologies". This was done in Protege 5.2.