Add support for predicate_type.

Recognise the `predicate_type` slot in mappings and mapping sets. Check
that it does not contain the illegal values `rdfs literal` and `composed
entity expression`.

Add a `predicate_type==` filter in SSSOM/T.

When producing OWL axioms from mappings in "direct" mode, use the value
of the `predicate_type` slot, if present, to determine the type of axiom
to generate.

core/src/main/java/org/incenp/obofoundry/sssom/Validator.java

@@ -38,6 +38,7 @@ public class Validator {
     public static final String MISSING_OBJECT_ID = "Missing object_id";
     public static final String MISSING_PREDICATE = "Missing predicate_id";
     public static final String MISSING_JUSTIFICATION = "Missing mapping_justification";
+    public static final String INVALID_PREDICATE_TYPE = "Invalid predicate_type";
 
     /**
      * Validates an individual mapping. This method checks that the slots that are
@@ -75,6 +76,11 @@ public String validate(Mapping mapping) {
             return MISSING_JUSTIFICATION;
         }
 
+        if ( mapping.getPredicateType() == EntityType.RDFS_LITERAL
+                || mapping.getPredicateType() == EntityType.COMPOSED_ENTITY_EXPRESSION ) {
+            return INVALID_PREDICATE_TYPE;
+        }
+
         return null;
     }
 }

core/src/main/lombok/org/incenp/obofoundry/sssom/model/Mapping.java

@@ -102,6 +102,9 @@ public class Mapping  {
     @JsonProperty("object_source_version")
     private String objectSourceVersion;
 
+    @JsonProperty("predicate_type")
+    private EntityType predicateType;
+
     @JsonProperty("mapping_provider")
     @URI
     private String mappingProvider;

core/src/main/lombok/org/incenp/obofoundry/sssom/model/MappingSet.java

@@ -81,6 +81,10 @@ public class MappingSet  {
     @Propagatable
     private String objectSourceVersion;
 
+    @JsonProperty("predicate_type")
+    @Propagatable
+    private EntityType predicateType;
+
     @JsonProperty("mapping_provider")
     @Propagatable
     @URI

core/src/test/java/org/incenp/obofoundry/sssom/ValidatorTest.java

@@ -27,7 +27,7 @@
 public class ValidatorTest {
 
     @Test
-    void testInvalidMappings() throws SSSOMFormatException, IOException {
+    void testMappingsWithMissingRequiredSlots() throws SSSOMFormatException, IOException {
         TSVReader reader = new TSVReader("src/test/resources/sets/test-missing-required-slots.sssom.tsv");
         reader.setValidationEnabled(false); // So we can check each mapping ourselves
         MappingSet ms = reader.read();
@@ -41,4 +41,18 @@ void testInvalidMappings() throws SSSOMFormatException, IOException {
             Assertions.assertEquals(expectedErrors[i], v.validate(ms.getMappings().get(i)));
         }
     }
+
+    @Test
+    void testMappingsWithInvalidPredicateTypes() throws SSSOMFormatException, IOException {
+        TSVReader reader = new TSVReader("src/test/resources/sets/test-predicate-types.sssom.tsv");
+        reader.setValidationEnabled(false);
+        MappingSet ms = reader.read();
+
+        String[] expectedErrors = { null, null, Validator.INVALID_PREDICATE_TYPE, Validator.INVALID_PREDICATE_TYPE };
+
+        Validator v = new Validator();
+        for ( int i = 0, n = ms.getMappings().size(); i < n; i++ ) {
+            Assertions.assertEquals(expectedErrors[i], v.validate(ms.getMappings().get(i)));
+        }
+    }
 }

core/src/test/resources/sets/test-predicate-types.sssom.tsv

@@ -0,0 +1,10 @@
+#curie_map:
+#  COMENT: https://example.com/entities/
+#  ORGENT: https://example.org/entities/
+#mapping_set_id: https://example.org/sets/test-predicate-types
+#license: https://creativecommons.org/licenses/by/4.0/
+subject_id	subject_label	predicate_id	object_id	object_label	mapping_justification	predicate_type
+ORGENT:0001	alice	skos:closeMatch	COMENT:0011	alpha	semapv:ManualMappingCuration	owl object property
+ORGENT:0002	bob	skos:closeMatch	COMENT:0012	beta	semapv:ManualMappingCuration	owl annotation property
+ORGENT:0004	daphne	skos:closeMatch	COMENT:0014	delta	semapv:ManualMappingCuration	rdfs literal
+ORGENT:0005	eve	skos:closeMatch	COMENT:0015	epsilon	semapv:ManualMappingCuration	composed entity expression

ext/src/main/antlr4/org/incenp/obofoundry/sssom/transform/parser/SSSOMTransform.g4

@@ -99,6 +99,7 @@ cardField : 'mapping_cardinality' | 'cardinality';
 
 entField  : 'object_type'
           | 'subject_type'
+          | 'predicate_type'
           ;
 
 idValue   : CURIE

ext/src/main/java/org/incenp/obofoundry/sssom/owl/DirectAxiomGenerator.java

@@ -21,6 +21,7 @@
 import java.util.HashSet;
 import java.util.Set;
 
+import org.incenp.obofoundry.sssom.model.EntityType;
 import org.incenp.obofoundry.sssom.model.Mapping;
 import org.incenp.obofoundry.sssom.transform.IMappingTransformer;
 import org.semanticweb.owlapi.model.IRI;
@@ -74,10 +75,31 @@ public DirectAxiomGenerator(OWLOntology ontology) {
     public OWLAxiom transform(Mapping mapping) {
         OWLAxiom axiom = null;
         String predicate = mapping.getPredicateId();
+        EntityType predicateType = mapping.getPredicateType();
         IRI subject = IRI.create(mapping.getSubjectId());
         IRI object = IRI.create(mapping.getObjectId());
 
-        if ( predicate.equals(OWL_EQUIVALENT_CLASS) ) {
+        /*
+         * The type of axiom to generate is dictated by the type of the predicate, which
+         * we obtain from (by order of precedence):
+         * 
+         * (1) the mapping itself, if it has a `predicate_type` slot set to either `owl
+         * annotation property` or `owl object property`;
+         * 
+         * (2) some built-in knowledge for a handful of predicates (owl:equivalentClass,
+         * rdfs:subClassOf, and the predicates listed in ANNOTATION_PREDICATES);
+         * 
+         * (3) the helper ontology, it it declares an annotation or object property with
+         * a matching IRI.
+         */
+
+        if ( predicateType == EntityType.OWL_ANNOTATION_PROPERTY ) {
+            axiom = factory.getOWLAnnotationAssertionAxiom(factory.getOWLAnnotationProperty(IRI.create(predicate)),
+                    subject, object);
+        } else if ( predicateType == EntityType.OWL_OBJECT_PROPERTY ) {
+            axiom = factory.getOWLSubClassOfAxiom(factory.getOWLClass(subject), factory.getOWLObjectSomeValuesFrom(
+                    factory.getOWLObjectProperty(IRI.create(predicate)), factory.getOWLClass(object)));
+        } else if ( predicate.equals(OWL_EQUIVALENT_CLASS) ) {
             axiom = factory.getOWLEquivalentClassesAxiom(factory.getOWLClass(object), factory.getOWLClass(object));
         } else if ( predicate.equals(RDFS_SUBCLASS_OF) ) {
             axiom = factory.getOWLSubClassOfAxiom(factory.getOWLClass(subject), factory.getOWLClass(object));

ext/src/main/java/org/incenp/obofoundry/sssom/transform/SSSOMTransformReader.java

@@ -989,6 +989,10 @@ public IMappingFilter visitEntityTypeFilterItem(SSSOMTransformParser.EntityTypeF
         case "subject_type":
             filter = (mapping) -> mapping.getSubjectType() == et;
             break;
+
+        case "predicate_type":
+            filter = (mapping) -> mapping.getPredicateType() == et;
+            break;
         }
 
         return addFilter(new NamedFilter(String.format("%s==%s", fieldName, value), filter));