code: public Ontology parseOBO(
  			BufferedReader oboFile,
  			String ontoName,
  			String ontoDescription
  			)
  					throws ParseException, IOException {
  
  		try {
  			OntologyFactory factory = OntoTools.getDefaultFactory();
  			Ontology ontology = factory.createOntology(ontoName, ontoDescription);
  
  			OboFileParser parser = new OboFileParser();
  
  			OboFileEventListener handler = new OboFileHandler(ontology);
  
  			parser.addOboFileEventListener(handler);
  			parser.parseOBO(oboFile);
  
  			return ontology;
  
  
  		} catch (AlreadyExistsException ex) {
  			throw new RuntimeException( "Duplication in ontology");
  		} catch (OntologyException ex) {
  			throw new RuntimeException(ex);
  		}
  
  	}
docs: Parse a OBO file and return its content as a BioJava Ontology object
  
  @param oboFile the file to be parsed
  @param ontoName
  @param ontoDescription
  
  @return the ontology represented as a BioJava ontology file
  @throws ParseException
  @throws IOException