update conversion of OBO alternate identifiers

as discussed in #317 (comment)
owlcs · Dec 24, 2014 · e1ec5d6 · e1ec5d6
1 parent a93a858
commit e1ec5d6
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diff --git a/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIObo2Owl.java b/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIObo2Owl.java
@@ -48,6 +48,7 @@
 import org.semanticweb.owlapi.model.OWLClassExpression;
 import org.semanticweb.owlapi.model.OWLDataFactory;
 import org.semanticweb.owlapi.model.OWLDocumentFormat;
+import org.semanticweb.owlapi.model.OWLEntity;
 import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
 import org.semanticweb.owlapi.model.OWLIndividual;
 import org.semanticweb.owlapi.model.OWLLiteral;
@@ -719,6 +720,13 @@ public OWLClassExpression trTermFrame(@Nonnull Frame termFrame) {
         for (String t : termFrame.getTags()) {
             // System.out.println("tag:"+tag);
             Collection<Clause> clauses = termFrame.getClauses(t);
+            if (OboFormatTag.TAG_ALT_ID.getTag().equals(t)) {
+                // Generate deprecated and replaced_by details for alternate identifier
+                Set<OWLAxiom> axioms = translateAltIds(clauses, termFrame.getId(), true);
+                if (!axioms.isEmpty()) {
+                    add(axioms);
+                }
+            }
             Set<OWLAxiom> axioms = trTermFrameClauses(cls, clauses, t);
             if (!axioms.isEmpty()) {
                 add(axioms);
@@ -728,6 +736,55 @@ public OWLClassExpression trTermFrame(@Nonnull Frame termFrame) {
     }
 
     /**
+     * Generate axioms for the alternate identifiers of an {@link OWLClass} or {@link OWLObjectProperty}.
+     * 
+     * @param clauses collection of alt_id clauses
+     * @param replacedBy OBO style ID
+     * @param isClass set to true if the alt_id is represents a class, false in case of an property
+     * @return set of axioms generated for the alt_id clauses
+     */
+    @Nonnull
+    protected Set<OWLAxiom> translateAltIds(
+            @Nonnull Collection<Clause> clauses, @Nonnull String replacedBy, 
+            boolean isClass) {
+        Set<OWLAxiom> axioms = new HashSet<>();
+        for(Clause clause : clauses) {
+            final String altId = clause.getValue(String.class);
+            if (altId != null) {
+                final OWLEntity altIdEntity;
+                if (isClass) {
+                    altIdEntity = trClass(altId);
+                }
+                else {
+                    IRI altIdIRI = oboIdToIRI(altId);
+                    altIdEntity = fac.getOWLObjectProperty(altIdIRI);
+                }
+                // entity declaration axiom
+                axioms.add(fac.getOWLDeclarationAxiom(altIdEntity));
+                // annotate as deprecated
+                axioms.add(fac.getOWLAnnotationAssertionAxiom(
+                    altIdEntity.getIRI(), fac.getOWLAnnotation(
+                        fac.getOWLDeprecated(),
+                        fac.getOWLLiteral(true))));
+                // annotate with replaced_by (IAO_0100001)
+                axioms.add(fac.getOWLAnnotationAssertionAxiom(
+                    altIdEntity.getIRI(),
+                    fac.getOWLAnnotation( fac.getOWLAnnotationProperty(
+                            Obo2OWLVocabulary.IRI_IAO_0100001.iri),
+                        fac.getOWLLiteral(replacedBy))));
+                // annotate with obo:IAO_0000231=obo:IAO_0000227
+                // 'has obsolescence reason' 'terms merged'
+                axioms.add(fac.getOWLAnnotationAssertionAxiom(
+                    altIdEntity.getIRI(), fac.getOWLAnnotation(
+                        fac.getOWLAnnotationProperty(
+                            Obo2OWLConstants.IRI_IAO_0000231),
+                        Obo2OWLConstants.IRI_IAO_0000227)));
+            }
+        }
+        return axioms;
+    }
+
+	/**
      * Tr term frame clauses.
      * 
      * @param cls

diff --git a/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIOwl2Obo.java b/oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIOwl2Obo.java
@@ -1605,6 +1605,14 @@ protected void tr(@Nonnull OWLDeclarationAxiom axiom) {
         if (set.isEmpty()) {
             return;
         }
+        // check whether the entity is an alt_id
+        Optional<String> altIdOptional = isAltId(set, entity);
+        if (altIdOptional.isPresent()) {
+            // TODO make sure that the alt_id is declared in the appropriate frame 
+            return;
+        }
+
+        // translate
         Frame f = null;
         if (entity instanceof OWLClass) {
             f = getTermFrame(entity.asOWLClass());
@@ -1630,6 +1638,50 @@ protected void tr(@Nonnull OWLDeclarationAxiom axiom) {
         }
     }
 
+    /**
+     * Check the annotations of entity for axioms declaring it to be an
+     * obsolete entity, with 'obsolescence reason' being 'term merge', and a 
+     * non-empty 'replaced by' literal.
+     * 
+     * @param annotations set of annotations for the entity
+     * @param entity
+     * @return replaced_by if it is an alt_id
+     */
+    @Nonnull
+    private Optional<String> isAltId(Set<OWLAnnotationAssertionAxiom> annotations, OWLEntity entity) {
+        String altId = null;
+        boolean isMerged = false;
+        boolean isDeprecated = false;
+        for (OWLAnnotationAssertionAxiom axiom : annotations) {
+            OWLAnnotationProperty prop = axiom.getProperty();
+            if (prop.isDeprecated()) {
+                isDeprecated = true;
+            }
+            else if (Obo2OWLConstants.IRI_IAO_0000231.equals(prop.getIRI())) {
+                OWLAnnotationValue value = axiom.getValue();
+                Optional<IRI> asIRI = value.asIRI();
+                if (asIRI.isPresent()) {
+                    isMerged = Obo2OWLConstants.IRI_IAO_0000227.equals(asIRI.get());
+                }
+            }
+            else if (Obo2OWLVocabulary.IRI_IAO_0100001.iri.equals(prop.getIRI())) {
+                OWLAnnotationValue value = axiom.getValue();
+                Optional<OWLLiteral> asLiteral = value.asLiteral();
+                if (asLiteral.isPresent()) {
+                    altId = asLiteral.get().getLiteral();
+                }
+            }
+        }
+        Optional<String> result;
+        if (altId != null && isMerged && isDeprecated) {
+            result = Optional.of(altId);
+        }
+        else {
+            result = Optional.absent();
+        }
+        return result;
+    }
+
     /**
      * Gets the identifier.
      * 

diff --git a/oboformat/src/main/java/org/obolibrary/obo2owl/Obo2OWLConstants.java b/oboformat/src/main/java/org/obolibrary/obo2owl/Obo2OWLConstants.java
@@ -23,6 +23,14 @@ public class Obo2OWLConstants {
     @Nonnull
     public static final String OIOVOCAB_IRI_PREFIX = "http://www.geneontology.org/formats/oboInOwl#";
 
+    /** IRI for the 'has obsolescence reason' annotation property */
+    @Nonnull
+    public static final IRI IRI_IAO_0000231 = IRI.create(DEFAULT_IRI_PREFIX+"IAO_0000231");
+
+    /** IRI for the 'terms merged' individual */
+    @Nonnull
+    public static final IRI IRI_IAO_0000227 = IRI.create(DEFAULT_IRI_PREFIX+"IAO_0000227");
+
     /**
      * @param d
      *        date to format