Include SubObjectPropertyOf axioms when reducing.

CHANGELOG.md

@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Bug was fixed that caused logical axioms with axiom annotations not to be processed correctly when merging axiom annotations [#1223]
 - Correctly merge unannotated and annotated duplicated axioms [#1239]
 - Fix reading of default queries from embedded Jar resources [#1212]
+- Subproperties being ignored when evaluating redundancy in `reduce` [#1014], [#1208]
 
 ## [1.9.7] - 2024-10-30
 

docs/examples/reduced-redundant-over-subproperties.ofn

@@ -0,0 +1,40 @@
+Prefix(:=<http://purl.obolibrary.org/obo/test.owl#>)
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(<http://purl.obolibrary.org/obo/test.owl>
+
+Declaration(Class(<http://purl.obolibrary.org/obo/Kupffer_cell>))
+Declaration(Class(<http://purl.obolibrary.org/obo/liver>))
+Declaration(Class(<http://purl.obolibrary.org/obo/liver_lobule>))
+Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/located_in>))
+Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/overlaps>))
+Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/part_of>))
+############################
+#   Object Properties
+############################
+
+# Object Property: <http://purl.obolibrary.org/obo/part_of> (<http://purl.obolibrary.org/obo/part_of>)
+
+SubObjectPropertyOf(<http://purl.obolibrary.org/obo/part_of> <http://purl.obolibrary.org/obo/overlaps>)
+
+
+############################
+#   Classes
+############################
+
+# Class: <http://purl.obolibrary.org/obo/Kupffer_cell> (<http://purl.obolibrary.org/obo/Kupffer_cell>)
+
+SubClassOf(<http://purl.obolibrary.org/obo/Kupffer_cell> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/located_in> <http://purl.obolibrary.org/obo/liver_lobule>))
+
+# Class: <http://purl.obolibrary.org/obo/liver_lobule> (<http://purl.obolibrary.org/obo/liver_lobule>)
+
+SubClassOf(<http://purl.obolibrary.org/obo/liver_lobule> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/part_of> <http://purl.obolibrary.org/obo/liver>))
+
+
+SubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/located_in> <http://purl.obolibrary.org/obo/part_of>) <http://purl.obolibrary.org/obo/located_in>)
+)

docs/examples/redundant-over-subproperties.ofn

@@ -0,0 +1,42 @@
+Prefix(:=<http://purl.obolibrary.org/obo/test.owl#>)
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+
+
+Ontology(<http://purl.obolibrary.org/obo/test.owl>
+
+Declaration(Class(<http://purl.obolibrary.org/obo/Kupffer_cell>))
+Declaration(Class(<http://purl.obolibrary.org/obo/liver>))
+Declaration(Class(<http://purl.obolibrary.org/obo/liver_lobule>))
+Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/located_in>))
+Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/overlaps>))
+Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/part_of>))
+############################
+#   Object Properties
+############################
+
+# Object Property: <http://purl.obolibrary.org/obo/part_of> (<http://purl.obolibrary.org/obo/part_of>)
+
+SubObjectPropertyOf(<http://purl.obolibrary.org/obo/part_of> <http://purl.obolibrary.org/obo/overlaps>)
+
+
+############################
+#   Classes
+############################
+
+# Class: <http://purl.obolibrary.org/obo/Kupffer_cell> (<http://purl.obolibrary.org/obo/Kupffer_cell>)
+
+SubClassOf(<http://purl.obolibrary.org/obo/Kupffer_cell> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/located_in> <http://purl.obolibrary.org/obo/liver>))
+SubClassOf(<http://purl.obolibrary.org/obo/Kupffer_cell> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/located_in> <http://purl.obolibrary.org/obo/liver_lobule>))
+
+# Class: <http://purl.obolibrary.org/obo/liver_lobule> (<http://purl.obolibrary.org/obo/liver_lobule>)
+
+SubClassOf(<http://purl.obolibrary.org/obo/liver_lobule> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/overlaps> <http://purl.obolibrary.org/obo/liver>))
+SubClassOf(<http://purl.obolibrary.org/obo/liver_lobule> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/part_of> <http://purl.obolibrary.org/obo/liver>))
+
+
+SubObjectPropertyOf(ObjectPropertyChain(<http://purl.obolibrary.org/obo/located_in> <http://purl.obolibrary.org/obo/part_of>) <http://purl.obolibrary.org/obo/located_in>)
+)

docs/reduce.md

@@ -15,4 +15,23 @@ Available options for `reduce`:
 ### Warning
 
 Reciprocal subclass axioms (e.g. `A SubClassOf B`, `B SubClassOf A`), entailing equivalence between `A` and `B`, may be removed by `reduce`. In this case it is important to
-assert an equivalence axiom (`A EquivalentTo B`) using the `reason` command before running reduce.
+assert an equivalence axiom (`A EquivalentTo B`) using the `reason` command before running reduce.
+
+### Subproperties and property chains
+
+For backwards compatibility reasons, by default subObjectPropertyOf axioms are ignored when evaluating the redundancy of subClassOf axioms. This means that, given the following example:
+
+```
+C SubClassOf P some D
+C SubClassOf Q some D
+P SubObjectPropertyOf Q
+```
+
+the first subClassOf axiom would by default _not_ be considered redundant and therefore _not_ be removed.
+
+To force the `reduce` command to factor in subproperties (including property chains) when evaluating redundancy, use the `--include-subproperties` option:
+
+    robot reduce --reasoner ELK \
+      --input redundant-over-subproperties.ofn \
+      --include-subproperties true \
+      --output results/reduced-redundant-over-subproperties.ofn

robot-command/src/main/java/org/obolibrary/robot/ReduceCommand.java

@@ -31,6 +31,11 @@ public ReduceCommand() {
         "preserve annotated axioms when removing redundant subclass axioms");
     o.addOption(
         "c", "named-classes-only", true, "only reduce subclass axioms between named classes");
+    o.addOption(
+        "s",
+        "include-subproperties",
+        true,
+        "take subproperties into account to evaluate redundancy");
     o.addOption("i", "input", true, "reduce ontology from a file");
     o.addOption("I", "input-iri", true, "reduce ontology from an IRI");
     o.addOption("o", "output", true, "save reduceed ontology to a file");

robot-core/src/main/java/org/obolibrary/robot/ReduceOperation.java

@@ -55,6 +55,7 @@ public static Map<String, String> getDefaultOptions() {
     Map<String, String> options = new HashMap<>();
     options.put("preserve-annotated-axioms", "false");
     options.put("named-classes-only", "false");
+    options.put("include-subproperties", "false");
     return options;
   }
 
@@ -87,7 +88,9 @@ public static void reduce(
     if (namedClassesOnly) {
       reduceNamedOnly(ontology, reasonerFactory, preserveAnnotatedAxioms);
     } else {
-      reduceAllClassExpressions(ontology, reasonerFactory, preserveAnnotatedAxioms);
+      boolean includeSubproperties = OptionsHelper.optionIsTrue(options, "include-subproperties");
+      reduceAllClassExpressions(
+          ontology, reasonerFactory, preserveAnnotatedAxioms, includeSubproperties);
     }
   }
 
@@ -97,21 +100,31 @@ public static void reduce(
    * @param ontology The ontology to reduce.
    * @param reasonerFactory The reasoner factory to use.
    * @param preserveAnnotatedAxioms Whether to not remove redundant, but annotated, axioms.
+   * @param includeSubproperties Whether to include subPropertyOf axioms (including property chains)
+   *     for evaluating redundancy.
    * @throws OWLOntologyCreationException on ontology problem
    */
   private static void reduceAllClassExpressions(
-      OWLOntology ontology, OWLReasonerFactory reasonerFactory, boolean preserveAnnotatedAxioms)
+      OWLOntology ontology,
+      OWLReasonerFactory reasonerFactory,
+      boolean preserveAnnotatedAxioms,
+      boolean includeSubproperties)
       throws OWLOntologyCreationException {
 
     OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
     OWLDataFactory dataFactory = manager.getOWLDataFactory();
 
     // we treat an axiom as redundant if its is redundant within the
     // subClassOf graph, including OP characteristic axioms (e.g. transitivity)
+    // and subproperty axioms
     OWLOntology subOntology = manager.createOntology();
     for (OWLAxiom a : ontology.getAxioms(Imports.INCLUDED)) {
       if (a instanceof OWLSubClassOfAxiom || a instanceof OWLObjectPropertyCharacteristicAxiom) {
         manager.addAxiom(subOntology, a);
+      } else if (includeSubproperties
+          && (a instanceof OWLSubObjectPropertyOfAxiom
+              || a instanceof OWLSubPropertyChainOfAxiom)) {
+        manager.addAxiom(subOntology, a);
       }
     }