OWLAP-183 Sub property axioms when converting from relationships.

AxiomRelationshipConversionService.convertRelationshipsToAxiom will now create SubObjectPropertyOf or SubDataPropertyOf axioms when converting a set of relationships to axioms if one of the parents are identified in the set of object property or data property concepts.

Author: kaicode

src/main/java/org/snomed/otf/owltoolkit/conversion/AxiomRelationshipConversionService.java

@@ -23,12 +23,27 @@ public class AxiomRelationshipConversionService {
 	private final OntologyService ontologyService;
 
 	private static final Logger LOGGER = LoggerFactory.getLogger(AxiomRelationshipConversionService.class);
+	private Collection<Long> objectAttributes;
+	private Collection<Long> dataAttributes;
 
 	public AxiomRelationshipConversionService(Set<Long> ungroupedAttributes) {
 		snomedTaxonomyLoader = new SnomedTaxonomyLoader();
 		ontologyService = new OntologyService(ungroupedAttributes);
 	}
 
+	/**
+	 * Use this constructor to enable generating SubObjectPropertyOf and SubDataPropertyOf axioms from relationships.
+	 * @param ungroupedAttributes
+	 * @param objectAttributes
+	 * @param dataAttributes
+	 */
+	public AxiomRelationshipConversionService(Set<Long> ungroupedAttributes, Collection<Long> objectAttributes, Collection<Long> dataAttributes) {
+		snomedTaxonomyLoader = new SnomedTaxonomyLoader();
+		ontologyService = new OntologyService(ungroupedAttributes);
+		this.objectAttributes = objectAttributes;
+		this.dataAttributes = dataAttributes;
+	}
+
 	/**
 	 * Converts an OWL Axiom expression String to an AxiomRepresentation containing a concept id or set of relationships for each side of the expression.
 	 * Currently supported axiom types are SubClassOf and EquivalentClasses.
@@ -172,8 +187,31 @@ public Map<Long, Set<AxiomRepresentation>> convertAxiomsToRelationships(Map<Long
 	}
 
 	public String convertRelationshipsToAxiom(AxiomRepresentation representation) {
-		OWLClassAxiom owlClassAxiom = ontologyService.createOwlClassAxiom(representation);
-		return owlClassAxiom.toString().replaceAll(CORE_COMPONENT_NAMESPACE_PATTERN, ":$1").replace(") )", "))");
+
+		// Identify and convert object and data property axioms
+		if (representation.getLeftHandSideNamedConcept() != null && representation.getRightHandSideRelationships() != null) {
+			List<Relationship> relationships = representation.getRightHandSideRelationships().get(0);
+			for (Relationship relationship : relationships) {
+				if (relationship.getTypeId() == Concepts.IS_A_LONG) {
+					if (objectAttributes != null && objectAttributes.contains(relationship.getDestinationId())) {
+						// Attributes will only have one parent
+						return axiomToString(ontologyService.createOwlSubObjectPropertyOfAxiom(representation.getLeftHandSideNamedConcept(), relationship.getDestinationId()));
+					} else if (dataAttributes != null && dataAttributes.contains(relationship.getDestinationId())) {
+						return axiomToString(ontologyService.createOwlSubDataPropertyOfAxiom(representation.getLeftHandSideNamedConcept(), relationship.getDestinationId()));
+					} else {
+						// If the first parent is not an attribute then the concept is not an attribute.
+						break;
+					}
+				}
+			}
+		}
+
+		// Normal axioms and GCI axioms go through here
+		return axiomToString(ontologyService.createOwlClassAxiom(representation));
+	}
+
+	public String axiomToString(OWLLogicalAxiom owlAxiom) {
+		return owlAxiom.toString().replaceAll(CORE_COMPONENT_NAMESPACE_PATTERN, ":$1").replace(") )", "))");
 	}
 
 	/**

src/main/java/org/snomed/otf/owltoolkit/ontology/OntologyService.java

@@ -112,22 +112,20 @@ public Map<Long, Set<OWLAxiom>> createAxiomsFromStatedRelationships(SnomedTaxono
 
 		Set<Long> descendants = snomedTaxonomy.getDescendants(conceptModelObjectAttribute);
 		for (Long objectAttributeId : descendants) {
-			OWLObjectProperty owlObjectProperty = getOwlObjectProperty(objectAttributeId);
 			for (Relationship relationship : snomedTaxonomy.getStatedRelationships(objectAttributeId)) {
 				if (relationship.getTypeId() == Concepts.IS_A_LONG && (relationship.getDestinationId() != Concepts.CONCEPT_MODEL_ATTRIBUTE_LONG) || !conceptModelObjectAttributePresent) {
 					axiomsMap.computeIfAbsent(objectAttributeId, (id) -> new HashSet<>())
-							.add(factory.getOWLSubObjectPropertyOfAxiom(owlObjectProperty, getOwlObjectProperty(relationship.getDestinationId())));
+							.add(createOwlSubObjectPropertyOfAxiom(objectAttributeId, relationship.getDestinationId()));
 				}
 			}
 		}
 
 		if (snomedTaxonomy.getAllConceptIds().contains(Concepts.CONCEPT_MODEL_DATA_ATTRIBUTE_LONG)) {
 			for (Long dataAttributeId : snomedTaxonomy.getDescendants(Concepts.CONCEPT_MODEL_DATA_ATTRIBUTE_LONG)) {
-				OWLDataProperty owlDataProperty = getOwlDataProperty(dataAttributeId);
 				for (Relationship relationship : snomedTaxonomy.getStatedRelationships(dataAttributeId)) {
 					if (relationship.getTypeId() == Concepts.IS_A_LONG) {
 						axiomsMap.computeIfAbsent(dataAttributeId, (id) -> new HashSet<>())
-								.add(factory.getOWLSubDataPropertyOfAxiom(owlDataProperty, getOwlDataProperty(relationship.getDestinationId())));
+								.add(createOwlSubDataPropertyOfAxiom(dataAttributeId, relationship.getDestinationId()));
 					}
 				}
 			}
@@ -194,6 +192,14 @@ public OWLClassAxiom createOwlClassAxiom(AxiomRepresentation axiomRepresentation
 		}
 	}
 
+	public OWLSubObjectPropertyOfAxiom createOwlSubObjectPropertyOfAxiom(Long objectAttributeId, long destinationId) {
+		return factory.getOWLSubObjectPropertyOfAxiom(getOwlObjectProperty(objectAttributeId), getOwlObjectProperty(destinationId));
+	}
+
+	public OWLSubDataPropertyOfAxiom createOwlSubDataPropertyOfAxiom(Long dataAttributeId, long destinationId) {
+		return factory.getOWLSubDataPropertyOfAxiom(getOwlDataProperty(dataAttributeId), getOwlDataProperty(destinationId));
+	}
+
 	private OWLClassExpression createOwlClassExpression(Long namedConcept, Map<Integer, List<Relationship>> relationships) {
 		if (namedConcept != null) {
 			return getOwlClass(namedConcept);