/** @param args */
public static void main(String[] args) {
String external = "http://purl.obolibrary.org/obo/iao/dev/external.owl";
String externalDerived = "http://purl.obolibrary.org/obo/iao/dev/externalDerived.owl";
String externalByHand = "http://purl.obolibrary.org/obo/iao/dev/externalByHand.owl";
String metaData = "http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl";
String reasonerName = "hermit";
String path = "C:/Documents and Settings/Jie/My Documents/Ontology/iao/releases/2012-01-05/";
String saveIaoFilename = path + "merged/iao-main-infer.owl";
String inferOntURIStr = "http://purl.obolibrary.org/obo/iao/dev/iao_inferredSuperClasses.owl";
String saveInferFilename = path + "merged/iao-inferredSuperClasses.owl";
// Get hold of an ontology manager
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
AutoIRIMapper mapper = new AutoIRIMapper(new File(path + "ontology/"), false);
manager.addIRIMapper(mapper);
OWLOntology iaoOnt = OntologyManipulator.load(path + "ontology/iao-main.owl", manager);
// OntologyManipulator.printPrefixNSs(manager, iaoOnt);
OWLDataFactory df = manager.getOWLDataFactory();
// get all imported ontologies
Set<OWLOntology> importOnts = iaoOnt.getImports();
// remove imports statements from the loaded ontology
for (OWLOntology importOnt : importOnts) {
IRI importOntIRI = importOnt.getOntologyID().getOntologyIRI();
if (importOntIRI.equals(IRI.create(metaData))
|| importOntIRI.equals(IRI.create(external))
|| importOntIRI.equals(IRI.create(externalByHand))
|| importOntIRI.equals(IRI.create(externalDerived))) {
RemoveImport ri = new RemoveImport(iaoOnt, df.getOWLImportsDeclaration(importOntIRI));
manager.applyChange(ri);
}
}
// merge the removed imported ontologies to the loaded one
for (OWLOntology importOnt : importOnts) {
IRI importOntIRI = importOnt.getOntologyID().getOntologyIRI();
if (importOntIRI.equals(IRI.create(metaData))
|| importOntIRI.equals(IRI.create(external))
|| importOntIRI.equals(IRI.create(externalByHand))
|| importOntIRI.equals(IRI.create(externalDerived))) {
// OntologyManipulator.printPrefixNSs(manager, importOnt);
iaoOnt = OntologyManipulator.mergeToTargetOnt(manager, iaoOnt, importOnt);
}
}
// generate the inferred hierarchy and clean the super classes
OWLReasoner reasoner = OWLReasonerRunner.runReasoner(manager, iaoOnt, reasonerName);
iaoOnt =
OWLReasonerRunner.getCleanedOntologyWithInferredSuperClasses(
manager, iaoOnt, inferOntURIStr, reasoner);
OntologyManipulator.saveToFile(manager, iaoOnt, saveIaoFilename);
if (manager.contains(IRI.create(inferOntURIStr))) {
OWLOntology inferOnt = manager.getOntology(IRI.create(inferOntURIStr));
OntologyManipulator.saveToFile(manager, inferOnt, saveInferFilename);
}
}
