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 <http://www.w3.org/1999/02/22-rdf-syntax-ns.rdf>\"\"\"");
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.