Allow arbitrary defined annotation properties as qualifier tags in OBO format

contract/src/test/java/org/obolibrary/oboformat/TagIRIsTest.java

@@ -0,0 +1,54 @@
+package org.obolibrary.oboformat;
+
+import org.junit.jupiter.api.Test;
+import org.semanticweb.owlapi.api.test.baseclasses.TestBase;
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.*;
+import org.semanticweb.owlapi.vocab.OWL2Datatype;
+
+import java.util.Collections;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+public class TagIRIsTest extends TestBase {
+
+    @Test
+    public void testTagIRIMapping() {
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLAnnotationProperty definition = factory.getOWLAnnotationProperty(IRI.create("http://purl.obolibrary.org/obo/IAO_0000115"));
+        OWLAnnotationProperty oioCreatedBy = factory.getOWLAnnotationProperty(IRI.create("http://www.geneontology.org/formats/oboInOwl#created_by"));
+        OWLAnnotationProperty oioInventedBy = factory.getOWLAnnotationProperty(IRI.create("http://www.geneontology.org/formats/oboInOwl#invented_by"));
+        OWLAnnotationProperty source = factory.getOWLAnnotationProperty(IRI.create("http://purl.obolibrary.org/obo/MYONT_20"));
+        OWLOntology ont = loadOntology("obo/tag_iris.obo", manager);
+        Set<OWLAxiom> axioms = ont.getAxioms();
+        OWLClass term1 = factory.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MYONT_1"));
+        OWLClass term2 = factory.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MYONT_2"));
+        OWLClass term3 = factory.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MYONT_3"));
+        OWLClass term4 = factory.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MYONT_4"));
+        assertTrue(axioms.contains(
+                factory.getOWLAnnotationAssertionAxiom(definition, term1.getIRI(), factory.getOWLLiteral("Definition of term one.", OWL2Datatype.XSD_STRING),
+                        Stream.of(
+                                        factory.getOWLAnnotation(factory.getRDFSComment(), factory.getOWLLiteral("Here is a sub-annotation.", OWL2Datatype.XSD_STRING)),
+                                        factory.getOWLAnnotation(factory.getRDFSSeeAlso(), factory.getOWLLiteral("A nested see also value.", OWL2Datatype.XSD_STRING)))
+                                .collect(Collectors.toSet())
+                )));
+        assertTrue(axioms.contains(
+                factory.getOWLAnnotationAssertionAxiom(factory.getRDFSSeeAlso(), term1.getIRI(), factory.getOWLLiteral("See also value.", OWL2Datatype.XSD_STRING))));
+        assertTrue(axioms.contains(
+                factory.getOWLAnnotationAssertionAxiom(definition, term2.getIRI(), factory.getOWLLiteral("Definition of term two.", OWL2Datatype.XSD_STRING),
+                        Collections.singleton(factory.getOWLAnnotation(source, factory.getOWLLiteral("A nested annotation value.", OWL2Datatype.XSD_STRING))))));
+        assertTrue(axioms.contains(
+                factory.getOWLAnnotationAssertionAxiom(definition, term3.getIRI(), factory.getOWLLiteral("Definition of term three.", OWL2Datatype.XSD_STRING),
+                        Collections.singleton(factory.getOWLAnnotation(source, factory.getOWLLiteral("A definition source value.", OWL2Datatype.XSD_STRING))))));
+        assertTrue(axioms.contains(
+                factory.getOWLAnnotationAssertionAxiom(oioCreatedBy, term3.getIRI(), factory.getOWLLiteral("goc:bro", OWL2Datatype.XSD_STRING))), "created_by is built in and should not be overridden by a typedef");
+        assertTrue(axioms.contains(
+                factory.getOWLAnnotationAssertionAxiom(definition, term4.getIRI(), factory.getOWLLiteral("Definition of term four.", OWL2Datatype.XSD_STRING),
+                        Collections.singleton(factory.getOWLAnnotation(oioInventedBy, factory.getOWLLiteral("An inventor value.", OWL2Datatype.XSD_STRING))))), "An undeclared tag should have oio namespace");
+
+    }
+}

contract/src/test/resources/obo/tag_iris.obo

@@ -0,0 +1,56 @@
+format-version: 1.2
+ontology: myont
+
+[Term]
+id: MYONT:1
+name: term one
+def: "Definition of term one." [] {comment="Here is a sub-annotation.", seeAlso="A nested see also value."}
+property_value: seeAlso "See also value." xsd:string
+
+[Term]
+id: MYONT:2
+name: term two
+def: "Definition of term two." [] {MYONT:20="A nested annotation value."}
+property_value: MYONT:21 "A top level annotation value." xsd:string
+
+[Term]
+id: MYONT:3
+name: term three
+def: "Definition of term three." [] {source="A definition source value."}
+intersection_of: MYONT:2 ! term two
+intersection_of: results_in_transport_across GO:0005739 ! mitochondrion
+created_by: goc:bro
+
+[Term]
+id: MYONT:4
+name: term four
+def: "Definition of term four." [] {invented_by="An inventor value."}
+
+[Typedef]
+id: source
+name: source
+xref: MYONT:20
+is_metadata_tag: true
+
+[Typedef]
+id: MYONT:21
+name: source2
+is_metadata_tag: true
+
+[Typedef]
+id: seeAlso
+name: see also
+xref: http://www.w3.org/2000/01/rdf-schema#seeAlso
+is_metadata_tag: true
+
+[Typedef]
+id: results_in_transport_across
+name: results in transport across
+namespace: external
+xref: RO:0002342
+
+[Typedef]
+id: created_by
+name: created by
+namespace: external
+xref: http://purl.org/dc/terms/creator

oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIObo2Owl.java

@@ -1,6 +1,7 @@
 package org.obolibrary.obo2owl;
 
 import static org.obolibrary.obo2owl.Obo2OWLConstants.DEFAULT_IRI_PREFIX;
+import static org.obolibrary.obo2owl.Obo2OWLConstants.OIOVOCAB_IRI_PREFIX;
 import static org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull;
 
 import java.io.File;
@@ -1518,6 +1519,15 @@ public static IRI trTagToIRI(String tag) {
         return iri;
     }
 
+    @Nonnull
+    private IRI trTagToIRIIncludingTypedefs(String tag) {
+        IRI iri = ANNOTATIONPROPERTYMAP.get(tag);
+        if (iri == null) {
+            iri = oboIdToIRI(tag, true);
+        }
+        return iri;
+    }
+
     /**
      * Translate tag to annotation prop.
      * 
@@ -1526,7 +1536,7 @@ public static IRI trTagToIRI(String tag) {
      */
     @Nonnull
     protected OWLAnnotationProperty trTagToAnnotationProp(@Nonnull String tag) {
-        IRI iri = trTagToIRI(tag);
+        IRI iri = trTagToIRIIncludingTypedefs(tag);
         OWLAnnotationProperty ap = fac.getOWLAnnotationProperty(iri);
         if (!apToDeclare.contains(ap)) {
             apToDeclare.add(ap);
@@ -1624,22 +1634,31 @@ protected OWLAnnotationValue trLiteral(@Nonnull Object inputValue) {
      */
     @Nonnull
     public IRI oboIdToIRI(@Nonnull String id) {
+        return oboIdToIRI(id, false);
+    }
+
+    private IRI oboIdToIRI(@Nonnull String id, boolean oboInOwlDefault) {
         IRI iri = idToIRICache.get(id);
         if (iri == null) {
-            iri = oboIdToIRI_load(id);
+            iri = oboIdToIRI_load(id, oboInOwlDefault);
             idToIRICache.put(id, iri);
         }
         return iri;
     }
 
+    @Nonnull
+    public IRI oboIdToIRI_load(@Nonnull String id) {
+        return oboIdToIRI_load(id, false);
+    }
+
     /**
      * Obo id to iri.
      * 
      * @param id the id
      * @return the iri
      */
     @Nonnull
-    public IRI oboIdToIRI_load(@Nonnull String id) {
+    public IRI oboIdToIRI_load(@Nonnull String id, boolean oboInOwlDefault) {
         if (id.contains(" ")) {
             LOG.error("id contains space: \"{}\"", id);
             throw new OWLParserException("spaces not allowed: '" + id + '\'');
@@ -1704,10 +1723,16 @@ public IRI oboIdToIRI_load(@Nonnull String id) {
             // if(id.contains("_"))
             // db += "_";
             localId = idParts[0];// Unprefixed-ID
+
         }
-        String uriPrefix = DEFAULT_IRI_PREFIX + db;
-        if (idSpaceMap.containsKey(db)) {
-            uriPrefix = idSpaceMap.get(db);
+        String uriPrefix;
+        if (oboInOwlDefault) {
+            uriPrefix = OIOVOCAB_IRI_PREFIX;
+        } else {
+            uriPrefix = DEFAULT_IRI_PREFIX + db;
+            if (idSpaceMap.containsKey(db)) {
+                uriPrefix = idSpaceMap.get(db);
+            }
         }
         String safeId;
         try {

oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIOwl2Obo.java

@@ -1869,6 +1869,8 @@ public static String owlObjectToTag(OWLObject obj) {
             String prefix = Obo2OWLConstants.OIOVOCAB_IRI_PREFIX;
             if (iri.startsWith(prefix)) {
                 tag = iri.substring(prefix.length());
+            } else {
+                tag = getIdentifier(iriObj);
             }
         }
         return tag;

oboformat/src/main/java/org/obolibrary/obo2owl/Obo2OWLConstants.java

@@ -55,6 +55,9 @@ public enum Obo2OWLVocabulary implements HasIRI {
         /**IRI_IAO_0100001*/    IRI_IAO_0100001(DEFAULT_IRI_PREFIX, "IAO_0100001", "term replaced by", OboFormatTag.TAG_REPLACED_BY.getTag()),
         /**IRI_OIO_shorthand*/  IRI_OIO_shorthand(OIOVOCAB_IRI_PREFIX, "shorthand", "shorthand", "shorthand"),
         /**IRI_OIO_consider*/   IRI_OIO_consider(OIOVOCAB_IRI_PREFIX, "consider", "consider", OboFormatTag.TAG_CONSIDER.getTag()),
+        /**IRI_OIO_id*/   IRI_OIO_id(OIOVOCAB_IRI_PREFIX, "id", "id", OboFormatTag.TAG_ID.getTag()),
+        /**IRI_OIO_created_by*/   IRI_OIO_created_by(OIOVOCAB_IRI_PREFIX, "created_by", "created by", OboFormatTag.TAG_CREATED_BY.getTag()),
+        /**IRI_OIO_creation_date*/   IRI_OIO_creation_date(OIOVOCAB_IRI_PREFIX, "creation_date", "creation date", OboFormatTag.TAG_CREATION_DATE.getTag()),
         /**IRI_OIO_hasOBOFormatVersion*/        IRI_OIO_hasOBOFormatVersion(OIOVOCAB_IRI_PREFIX, "hasOBOFormatVersion", "has_obo_format_version", OboFormatTag.TAG_FORMAT_VERSION.getTag()),
         /**IRI_OIO_treatXrefsAsIsA*/            IRI_OIO_treatXrefsAsIsA(OIOVOCAB_IRI_PREFIX, "treat-xrefs-as-is_a", "treat-xrefs-as-is_a", OboFormatTag.TAG_TREAT_XREFS_AS_IS_A.getTag()),
         /**IRI_OIO_treatXrefsAsHasSubClass*/    IRI_OIO_treatXrefsAsHasSubClass(OIOVOCAB_IRI_PREFIX, "treat-xrefs-as-has-subclass", "treat-xrefs-as-has-subclass", OboFormatTag.TAG_TREAT_XREFS_AS_HAS_SUBCLASS.getTag()),