Add more efficient mode for reduce when only considering named classes.

docs/reduce.md

@@ -7,3 +7,12 @@ ROBOT can be used to remove redundant subClassOf axioms:
       --output results/reduced.owl
 
 See [reason](/reason) for details on supported reasoners (EMR is not supported in `reduce`).
+
+Available options for `reduce`:
+* `--preserve-annotated-axioms`: if set to true, axioms that have axiom annotations will not be removed, even if found to be redundant (default `false`).
+* `--named-classes-only`: if set to true, only subclass axioms between named classes will be checked for redundancy. Anonymous class expressions will be ignored (default `false`).
+
+### 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.

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

@@ -29,6 +29,8 @@ public ReduceCommand() {
         "preserve-annotated-axioms",
         true,
         "preserve annotated axioms when removing redundant subclass axioms");
+    o.addOption(
+        "c", "named-classes-only", true, "only reduce subclass axioms between named classes");
     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

@@ -2,26 +2,12 @@
 
 import com.google.common.collect.HashMultimap;
 import com.google.common.collect.Multimap;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-import java.util.UUID;
+import java.util.*;
 import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.model.AxiomType;
-import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLAxiom;
-import org.semanticweb.owlapi.model.OWLClass;
-import org.semanticweb.owlapi.model.OWLClassExpression;
-import org.semanticweb.owlapi.model.OWLDataFactory;
-import org.semanticweb.owlapi.model.OWLObjectPropertyCharacteristicAxiom;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.semanticweb.owlapi.model.OWLOntologyManager;
-import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
+import org.semanticweb.owlapi.model.*;
 import org.semanticweb.owlapi.model.parameters.Imports;
 import org.semanticweb.owlapi.reasoner.Node;
+import org.semanticweb.owlapi.reasoner.NodeSet;
 import org.semanticweb.owlapi.reasoner.OWLReasoner;
 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
 import org.slf4j.Logger;
@@ -38,15 +24,15 @@
  *
  * <h2>Implementation</h2>
  *
- * Because an OWL reasoner will only return named (non-anonymous) superclasses, we add a
+ * <p>Because an OWL reasoner will only return named (non-anonymous) superclasses, we add a
  * pre-processing step, where for each class C appearing in either LHS or RHS of a SubClassOf
  * expression, if C is anonymous, we create a named class C' and add a temporary axioms <code>
  * EquivalentClasses(C' C)</code>, which is later removed as a post-processing step. When performing
  * reasoner tests, we can then substitute C for C'
  *
  * <h2>GENERAL CLASS INCLUSION AXIOMS</h2>
  *
- * We make a special additional case of redunancy, as in the following example: <code>
+ * <p>We make a special additional case of redunancy, as in the following example: <code>
  * 1. (hand and part-of some human) SubClassOf part-of some forelimb
  * 2. hand SubClassOf part-of some forelimb
  * </code> Here we treat axiom 1 as redundant, but this is not detected by the algorithm above,
@@ -68,6 +54,7 @@ public class ReduceOperation {
   public static Map<String, String> getDefaultOptions() {
     Map<String, String> options = new HashMap<>();
     options.put("preserve-annotated-axioms", "false");
+    options.put("named-classes-only", "false");
     return options;
   }
 
@@ -94,6 +81,27 @@ public static void reduce(OWLOntology ontology, OWLReasonerFactory reasonerFacto
   public static void reduce(
       OWLOntology ontology, OWLReasonerFactory reasonerFactory, Map<String, String> options)
       throws OWLOntologyCreationException {
+    boolean preserveAnnotatedAxioms =
+        OptionsHelper.optionIsTrue(options, "preserve-annotated-axioms");
+    boolean namedClassesOnly = OptionsHelper.optionIsTrue(options, "named-classes-only");
+    if (namedClassesOnly) {
+      reduceNamedOnly(ontology, reasonerFactory, preserveAnnotatedAxioms);
+    } else {
+      reduceAllClassExpressions(ontology, reasonerFactory, preserveAnnotatedAxioms);
+    }
+  }
+
+  /**
+   * Remove redundant SubClassOf axioms.
+   *
+   * @param ontology The ontology to reduce.
+   * @param reasonerFactory The reasoner factory to use.
+   * @param preserveAnnotatedAxioms Whether to not remove redundant, but annotated, axioms.
+   * @throws OWLOntologyCreationException on ontology problem
+   */
+  private static void reduceAllClassExpressions(
+      OWLOntology ontology, OWLReasonerFactory reasonerFactory, boolean preserveAnnotatedAxioms)
+      throws OWLOntologyCreationException {
 
     OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
     OWLDataFactory dataFactory = manager.getOWLDataFactory();
@@ -166,7 +174,7 @@ public static void reduce(
 
     Set<OWLSubClassOfAxiom> rmAxioms = new HashSet<>();
     for (OWLSubClassOfAxiom ax : assertedSubClassAxioms) {
-      if (OptionsHelper.optionIsTrue(options, "preserve-annotated-axioms")) {
+      if (preserveAnnotatedAxioms) {
         if (ax.getAnnotations().size() > 0) {
           logger.debug("Protecting axiom with annotations: " + ax);
           continue;
@@ -254,6 +262,7 @@ public static void reduce(
     for (OWLAxiom ax : rmAxioms) {
       manager.removeAxiom(ontology, ax);
     }
+    reasoner.dispose();
   }
 
   /**
@@ -279,4 +288,93 @@ private static OWLClass mapClass(
     }
     return rxmap.get(x);
   }
+
+  /**
+   * Remove redundant SubClassOf axioms, only considering named classes. When only considering named
+   * classes, a somewhat more efficient algorithm can be used.
+   *
+   * @param ontology The ontology to reduce.
+   * @param reasonerFactory The reasoner factory to use.
+   * @param preserveAnnotatedAxioms Whether to not remove redundant, but annotated, axioms.
+   */
+  private static void reduceNamedOnly(
+      OWLOntology ontology, OWLReasonerFactory reasonerFactory, boolean preserveAnnotatedAxioms) {
+    // Map<superclass, Map<subclass, axioms>>
+    Map<OWLClass, Map<OWLClass, Set<OWLSubClassOfAxiom>>> assertions = new HashMap<>();
+    Set<OWLSubClassOfAxiom> assertedSubClassAxioms = ontology.getAxioms(AxiomType.SUBCLASS_OF);
+    for (OWLSubClassOfAxiom ax : assertedSubClassAxioms) {
+      if (!ax.getSubClass().isAnonymous() && !ax.getSuperClass().isAnonymous()) {
+        OWLClass subclass = ax.getSubClass().asOWLClass();
+        OWLClass superclass = ax.getSuperClass().asOWLClass();
+        if (!assertions.containsKey(superclass)) {
+          assertions.put(superclass, new HashMap<>());
+        }
+        Map<OWLClass, Set<OWLSubClassOfAxiom>> subMap = assertions.get(superclass);
+        if (!subMap.containsKey(subclass)) {
+          subMap.put(subclass, new HashSet<>());
+        }
+        Set<OWLSubClassOfAxiom> axioms = subMap.get(subclass);
+        axioms.add(ax);
+      }
+    }
+    OWLReasoner reasoner = reasonerFactory.createReasoner(ontology);
+    if (!reasoner.isConsistent()) {
+      logger.info("Ontology is not consistent!");
+      return;
+    }
+    Node<OWLClass> unsatisfiableClasses = reasoner.getUnsatisfiableClasses();
+    if (unsatisfiableClasses.getSize() > 1) {
+      logger.info(
+          "There are {} unsatisfiable classes in the ontology.", unsatisfiableClasses.getSize());
+      for (OWLClass cls : unsatisfiableClasses) {
+        if (!cls.isOWLNothing()) {
+          logger.info("    unsatisfiable: " + cls.getIRI());
+        }
+      }
+    }
+    Set<OWLSubClassOfAxiom> nonredundant = new HashSet<>();
+    Set<Node<OWLClass>> alreadySeen = new HashSet<>();
+    findNonRedundant(reasoner.getTopClassNode(), reasoner, assertions, nonredundant, alreadySeen);
+    OWLOntologyManager manager = ontology.getOWLOntologyManager();
+    for (OWLSubClassOfAxiom ax : assertedSubClassAxioms) {
+      if (!ax.getSubClass().isAnonymous() && !ax.getSuperClass().isAnonymous()) {
+        if (preserveAnnotatedAxioms) {
+          if (ax.getAnnotations().size() > 0) {
+            logger.debug("Protecting axiom with annotations: " + ax);
+            continue;
+          }
+        }
+        if (!nonredundant.contains(ax)) {
+          manager.removeAxiom(ontology, ax);
+        }
+      }
+    }
+    reasoner.dispose();
+  }
+
+  private static void findNonRedundant(
+      Node<OWLClass> node,
+      OWLReasoner reasoner,
+      Map<OWLClass, Map<OWLClass, Set<OWLSubClassOfAxiom>>> assertions,
+      Set<OWLSubClassOfAxiom> nonredundant,
+      Set<Node<OWLClass>> alreadySeen) {
+    if (!alreadySeen.contains(node)) {
+      NodeSet<OWLClass> subclasses = reasoner.getSubClasses(node.getRepresentativeElement(), true);
+      for (OWLClass superclass : node.getEntities()) {
+        for (OWLClass subclass : subclasses.getFlattened()) {
+          if (assertions.containsKey(superclass)) {
+            Map<OWLClass, Set<OWLSubClassOfAxiom>> subclassAxiomsBySubclass =
+                assertions.get(superclass);
+            if (subclassAxiomsBySubclass.containsKey(subclass)) {
+              nonredundant.addAll(subclassAxiomsBySubclass.get(subclass));
+            }
+          }
+        }
+      }
+      alreadySeen.add(node);
+      for (Node<OWLClass> subclassNode : subclasses.getNodes()) {
+        findNonRedundant(subclassNode, reasoner, assertions, nonredundant, alreadySeen);
+      }
+    }
+  }
 }

robot-core/src/test/java/org/obolibrary/robot/ReduceOperationTest.java

@@ -29,6 +29,16 @@ public void testRemoveRedundantSubClassAxiomsPreserveAnnotated()
 
     ReduceOperation.reduce(reasoned, reasonerFactory, options);
     assertIdentical("/without_redundant_subclasses.owl", reasoned);
+
+    OWLOntology reasoned2 = loadOntology("/redundant_subclasses.owl");
+
+    Map<String, String> options2 = new HashMap<String, String>();
+    options2.put("remove-redundant-subclass-axioms", "true");
+    options2.put("preserve-annotated-axioms", "true");
+    options2.put("named-classes-only", "true");
+
+    ReduceOperation.reduce(reasoned2, reasonerFactory, options2);
+    assertIdentical("/without_redundant_subclasses.owl", reasoned2);
   }
 
   @Test
@@ -156,4 +166,22 @@ public void testReduceDomainCase() throws IOException, OWLOntologyCreationExcept
     ReduceOperation.reduce(reasoned, reasonerFactory, options);
     assertIdentical("/reduce-domain-test.owl", reasoned);
   }
+
+  /** Test reduce only named classes vs. including expressions */
+  @Test
+  public void testReducedNamedOnly() throws OWLOntologyCreationException, IOException {
+    OWLReasonerFactory reasonerFactory = new org.semanticweb.elk.owlapi.ElkReasonerFactory();
+
+    OWLOntology ontologyA = loadOntology("/reduce-named-only-test.ofn");
+    Map<String, String> optionsA = new HashMap<String, String>();
+    optionsA.put("named-classes-only", "true");
+    ReduceOperation.reduce(ontologyA, reasonerFactory, optionsA);
+    assertIdentical("/reduce-named-only-test-named-only-true-reduced.ofn", ontologyA);
+
+    OWLOntology ontologyB = loadOntology("/reduce-named-only-test.ofn");
+    Map<String, String> optionsB = new HashMap<String, String>();
+    optionsB.put("named-classes-only", "false");
+    ReduceOperation.reduce(ontologyB, reasonerFactory, optionsB);
+    assertIdentical("/reduce-named-only-test-named-only-false-reduced.ofn", ontologyB);
+  }
 }

robot-core/src/test/resources/reduce-named-only-test-named-only-false-reduced.ofn

@@ -0,0 +1,38 @@
+Prefix(:=<http://robot.obolibrary.org/reduce/test#>)
+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://robot.obolibrary.org/reduce/test>
+
+Declaration(Class(<http://robot.obolibrary.org/reduce/test/A>))
+Declaration(Class(<http://robot.obolibrary.org/reduce/test/B>))
+Declaration(Class(<http://robot.obolibrary.org/reduce/test/C>))
+Declaration(Class(<http://robot.obolibrary.org/reduce/test/D>))
+Declaration(ObjectProperty(<http://robot.obolibrary.org/reduce/test/r>))
+
+############################
+#   Classes
+############################
+
+# Class: <http://robot.obolibrary.org/reduce/test/A> (<http://robot.obolibrary.org/reduce/test/A>)
+
+SubClassOf(<http://robot.obolibrary.org/reduce/test/A> ObjectSomeValuesFrom(<http://robot.obolibrary.org/reduce/test/r> <http://robot.obolibrary.org/reduce/test/C>))
+
+# Class: <http://robot.obolibrary.org/reduce/test/B> (<http://robot.obolibrary.org/reduce/test/B>)
+
+SubClassOf(<http://robot.obolibrary.org/reduce/test/B> <http://robot.obolibrary.org/reduce/test/A>)
+
+# Class: <http://robot.obolibrary.org/reduce/test/C> (<http://robot.obolibrary.org/reduce/test/C>)
+
+SubClassOf(<http://robot.obolibrary.org/reduce/test/C> <http://robot.obolibrary.org/reduce/test/B>)
+
+# Class: <http://robot.obolibrary.org/reduce/test/D> (<http://robot.obolibrary.org/reduce/test/D>)
+
+SubClassOf(<http://robot.obolibrary.org/reduce/test/D> <http://robot.obolibrary.org/reduce/test/C>)
+
+
+)

robot-core/src/test/resources/reduce-named-only-test-named-only-true-reduced.ofn

@@ -0,0 +1,40 @@
+Prefix(:=<http://robot.obolibrary.org/reduce/test#>)
+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://robot.obolibrary.org/reduce/test>
+
+Declaration(Class(<http://robot.obolibrary.org/reduce/test/A>))
+Declaration(Class(<http://robot.obolibrary.org/reduce/test/B>))
+Declaration(Class(<http://robot.obolibrary.org/reduce/test/C>))
+Declaration(Class(<http://robot.obolibrary.org/reduce/test/D>))
+Declaration(ObjectProperty(<http://robot.obolibrary.org/reduce/test/r>))
+
+############################
+#   Classes
+############################
+
+# Class: <http://robot.obolibrary.org/reduce/test/A> (<http://robot.obolibrary.org/reduce/test/A>)
+
+SubClassOf(<http://robot.obolibrary.org/reduce/test/A> ObjectSomeValuesFrom(<http://robot.obolibrary.org/reduce/test/r> <http://robot.obolibrary.org/reduce/test/C>))
+
+# Class: <http://robot.obolibrary.org/reduce/test/B> (<http://robot.obolibrary.org/reduce/test/B>)
+
+SubClassOf(<http://robot.obolibrary.org/reduce/test/B> <http://robot.obolibrary.org/reduce/test/A>)
+SubClassOf(<http://robot.obolibrary.org/reduce/test/B> ObjectSomeValuesFrom(<http://robot.obolibrary.org/reduce/test/r> <http://robot.obolibrary.org/reduce/test/C>))
+
+# Class: <http://robot.obolibrary.org/reduce/test/C> (<http://robot.obolibrary.org/reduce/test/C>)
+
+SubClassOf(<http://robot.obolibrary.org/reduce/test/C> <http://robot.obolibrary.org/reduce/test/B>)
+
+# Class: <http://robot.obolibrary.org/reduce/test/D> (<http://robot.obolibrary.org/reduce/test/D>)
+
+SubClassOf(<http://robot.obolibrary.org/reduce/test/D> <http://robot.obolibrary.org/reduce/test/C>)
+SubClassOf(<http://robot.obolibrary.org/reduce/test/D> ObjectSomeValuesFrom(<http://robot.obolibrary.org/reduce/test/r> <http://robot.obolibrary.org/reduce/test/C>))
+
+
+)

robot-core/src/test/resources/reduce-named-only-test.ofn

@@ -0,0 +1,41 @@
+Prefix(:=<http://robot.obolibrary.org/reduce/test#>)
+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://robot.obolibrary.org/reduce/test>
+
+Declaration(Class(<http://robot.obolibrary.org/reduce/test/A>))
+Declaration(Class(<http://robot.obolibrary.org/reduce/test/B>))
+Declaration(Class(<http://robot.obolibrary.org/reduce/test/C>))
+Declaration(Class(<http://robot.obolibrary.org/reduce/test/D>))
+Declaration(ObjectProperty(<http://robot.obolibrary.org/reduce/test/r>))
+
+############################
+#   Classes
+############################
+
+# Class: <http://robot.obolibrary.org/reduce/test/A> (<http://robot.obolibrary.org/reduce/test/A>)
+
+SubClassOf(<http://robot.obolibrary.org/reduce/test/A> ObjectSomeValuesFrom(<http://robot.obolibrary.org/reduce/test/r> <http://robot.obolibrary.org/reduce/test/C>))
+
+# Class: <http://robot.obolibrary.org/reduce/test/B> (<http://robot.obolibrary.org/reduce/test/B>)
+
+SubClassOf(<http://robot.obolibrary.org/reduce/test/B> <http://robot.obolibrary.org/reduce/test/A>)
+SubClassOf(<http://robot.obolibrary.org/reduce/test/B> ObjectSomeValuesFrom(<http://robot.obolibrary.org/reduce/test/r> <http://robot.obolibrary.org/reduce/test/C>))
+
+# Class: <http://robot.obolibrary.org/reduce/test/C> (<http://robot.obolibrary.org/reduce/test/C>)
+
+SubClassOf(<http://robot.obolibrary.org/reduce/test/C> <http://robot.obolibrary.org/reduce/test/B>)
+
+# Class: <http://robot.obolibrary.org/reduce/test/D> (<http://robot.obolibrary.org/reduce/test/D>)
+
+SubClassOf(<http://robot.obolibrary.org/reduce/test/D> <http://robot.obolibrary.org/reduce/test/B>)
+SubClassOf(<http://robot.obolibrary.org/reduce/test/D> <http://robot.obolibrary.org/reduce/test/C>)
+SubClassOf(<http://robot.obolibrary.org/reduce/test/D> ObjectSomeValuesFrom(<http://robot.obolibrary.org/reduce/test/r> <http://robot.obolibrary.org/reduce/test/C>))
+
+
+)