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Update operations can be executed within the standard command framework of OntoBroker. The wrapper command sparqlupdate takes exactly one argument which specifies the SPARQL Update string. For example:

ontologyManager.execute("sparqlupdate \"\"\"CLEAR DEFAULT; LOAD <>\"\"\"");

The return value will be Boolean. TRUE in case of success, otherwise an exception is thrown. The update operations are also available via the SPARQL endpoint.