Java Code Examples for org.semanticweb.owlapi.model.OWLOntology#getImportsDeclarations()
The following examples show how to use
org.semanticweb.owlapi.model.OWLOntology#getImportsDeclarations() .
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Example 1
| Source File: OntologyMetadata.java From owltools with BSD 3-Clause "New" or "Revised" License | 6 votes |
|
public OntologyMetadata(OWLOntology ont) {
super();
OWLOntologyID id = ont.getOntologyID();
if (id.getOntologyIRI().isPresent())
ontologyIRI = id.getOntologyIRI().get().toString();
if (id.getVersionIRI().isPresent())
versionIRI = id.getVersionIRI().get().toString();
importDirectives = new HashSet<String>();
for (OWLImportsDeclaration oid : ont.getImportsDeclarations()) {
importDirectives.add(oid.getIRI().toString());
}
classCount = ont.getClassesInSignature().size();
namedIndividualCount = ont.getIndividualsInSignature().size();
axiomCount = ont.getAxiomCount();
annotations = new HashSet<OntologyAnnotation>();
for (OWLAnnotation ann : ont.getAnnotations()) {
annotations.add(new OntologyAnnotation(ann));
}
}
Example 2
| Source File: OwlOntologyProducer.java From SciGraph with Apache License 2.0 | 6 votes |
|
void addOntologyStructure(OWLOntologyManager manager, OWLOntology ontology) {
long parent = graph.createNode(OwlApiUtils.getIri(ontology));
graph.addLabel(parent, OwlLabels.OWL_ONTOLOGY);
for (OWLImportsDeclaration importDeclaration : ontology.getImportsDeclarations()) {
OWLOntology childOnt = manager.getImportedOntology(importDeclaration);
if (null == childOnt) {
// TODO: Why is childOnt sometimes null (when importing rdf)?
continue;
}
long child = graph.createNode(OwlApiUtils.getIri(childOnt));
graph.addLabel(parent, OwlLabels.OWL_ONTOLOGY);
if (graph.getRelationship(child, parent, OwlRelationships.RDFS_IS_DEFINED_BY).isPresent()) {
continue;
}
graph.createRelationship(child, parent, OwlRelationships.RDFS_IS_DEFINED_BY);
addOntologyStructure(manager, childOnt);
}
}
Example 3
| Source File: OWLGraphWrapperBasic.java From owltools with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
public void mergeOntology(OWLOntology extOnt, LabelPolicy labelPolicy) throws OWLOntologyCreationException {
OWLOntologyManager manager = getManager();
LOG.info("Merging "+extOnt+" policy: "+labelPolicy);
for (OWLAxiom axiom : extOnt.getAxioms()) {
if (labelPolicy != LabelPolicy.ALLOW_DUPLICATES) {
if (axiom instanceof OWLAnnotationAssertionAxiom) {
OWLAnnotationAssertionAxiom aa = (OWLAnnotationAssertionAxiom)axiom;
if (aa.getProperty().isLabel()) {
OWLAnnotationSubject subj = aa.getSubject();
if (subj instanceof IRI) {
Optional<OWLLiteral> label = null;
for (OWLAnnotationAssertionAxiom a1 : sourceOntology.getAnnotationAssertionAxioms(subj)) {
if (a1.getProperty().isLabel()) {
label = a1.getValue().asLiteral();
}
}
if (label != null && label.isPresent()) {
if (labelPolicy == LabelPolicy.PRESERVE_SOURCE) {
LOG.info("Preserving existing label:" +subj+" "+label+" // ditching: "+axiom);
continue;
}
if (labelPolicy == LabelPolicy.PRESERVE_EXT) {
LOG.info("Replacing:" +subj+" "+label+" with: "+axiom);
LOG.error("NOT IMPLEMENTED");
}
}
}
}
}
}
manager.applyChange(new AddAxiom(sourceOntology, axiom));
}
for (OWLImportsDeclaration oid: extOnt.getImportsDeclarations()) {
manager.applyChange(new AddImport(sourceOntology, oid));
}
addCommentToOntology(sourceOntology, "Includes "+summarizeOntology(extOnt));
}
Example 4
| Source File: OWLGraphManipulator.java From owltools with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
/**
* Merges {@code OWLAxiom}s from the import ontology closure, with the source ontology.
* This method is similar to {@link OWLGraphWrapperBasic#mergeImportClosure(boolean)},
* except that: i) an {@code OWLAxiom} will be added to the source ontology only if
* it is not already present in the source (without taking annotations into account);
* ii) a check is performed to ensure that there will not be more than
* one annotation axiom for a given subject, when the annotation property
* corresponds to a tag with max cardinality one in OBO format
* (see {@code org.obolibrary.oboformat.model.Frame#check()}). As for
* {@link OWLGraphWrapperBasic#mergeImportClosure(boolean)}, annotations on the ontology
* itself are not imported, and the import declarations are removed after execution.
*/
private void mergeImportClosure() {
log.info("Merging axioms from import closure with source ontology...");
OWLOntology sourceOnt = this.getOwlGraphWrapper().getSourceOntology();
//the method OWLOntology.containsAxiomIgnoreAnnotations is really
//not well optimized, so we get all OWLAxioms without annotations
//from the source ontology.
log.debug("Retrieving OWLAxioms without annotations from source ontology...");
Set<OWLAxiom> sourceAxiomsNoAnnots = new HashSet<OWLAxiom>();
for (OWLAxiom ax: sourceOnt.getAxioms()) {
sourceAxiomsNoAnnots.add(ax.getAxiomWithoutAnnotations());
}
if (log.isDebugEnabled()) {
log.debug(sourceAxiomsNoAnnots.size() + " axioms without annotations retrieved " +
"over " + sourceOnt.getAxiomCount() + " axioms.");
}
for (OWLOntology importedOnt: sourceOnt.getImportsClosure()) {
if (importedOnt.equals(sourceOnt)) {
continue;
}
log.info("Merging " + importedOnt);
// OWLDataFactory df = sourceOnt.getOWLOntologyManager().getOWLDataFactory();
// OWLAnnotationProperty p =
// df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI());
// OWLLiteral v = df.getOWLLiteral("Imported " + importedOnt);
// OWLAnnotation ann = df.getOWLAnnotation(p, v);
// AddOntologyAnnotation addAnn =
// new AddOntologyAnnotation(sourceOnt, ann);
// sourceOnt.getOWLOntologyManager().applyChange(addAnn);
//filter the axioms imported to avoid redundancy (too bad there is not
//a method OWLOntology.getAxiomsIgnoreAnnotations())
int importedAxiomCount = 0;
importAxioms: for (OWLAxiom importedAx: importedOnt.getAxioms()) {
if (sourceAxiomsNoAnnots.contains(importedAx.getAxiomWithoutAnnotations())) {
continue importAxioms;
}
//if it is an annotation axion, we need to ensure that
//there will not be more than one axiom for a given subject,
//when the annotation corresponds to a tag with max cardinality one
//in OBO format (see org.obolibrary.oboformat.model.Frame#check()).
if (importedAx instanceof OWLAnnotationAssertionAxiom) {
OWLAnnotationAssertionAxiom castAx =
(OWLAnnotationAssertionAxiom) importedAx;
if (maxOneCardinalityAnnots.contains(
castAx.getProperty().getIRI().toString()) ||
maxOneCardinalityAnnots.contains(
this.getOwlGraphWrapper().getIdentifier(
castAx.getProperty()))) {
//check whether we have an annotation for the same subject
//in the source ontology.
for (OWLAnnotationAssertionAxiom sourceAnnotAx:
sourceOnt.getAnnotationAssertionAxioms(
castAx.getSubject())) {
if (sourceAnnotAx.getProperty().equals(
castAx.getProperty())) {
//discard the axiom from import ontology, there is already
//an annotation with same property on same subject
log.trace("Discarding axiom: " + castAx);
continue importAxioms;
}
}
}
}
//all verifications passed, include the axiom
importedAxiomCount++;
sourceAxiomsNoAnnots.add(importedAx.getAxiomWithoutAnnotations());
sourceOnt.getOWLOntologyManager().addAxiom(sourceOnt, importedAx);
}
log.info(importedAxiomCount + " axioms imported.");
}
//remove the import declarations
Set<OWLImportsDeclaration> oids = sourceOnt.getImportsDeclarations();
for (OWLImportsDeclaration oid : oids) {
RemoveImport ri = new RemoveImport(sourceOnt, oid);
sourceOnt.getOWLOntologyManager().applyChange(ri);
}
log.info("Done merging axioms.");
}
