🌱 Added missing file

mowl/datasets/builtin/subsumption.py

@@ -0,0 +1,96 @@
+from ..base import RemoteDataset, OWLClasses
+from deprecated.sphinx import versionadded
+import os
+
+import java
+from org.semanticweb.owlapi.apibinding import OWLManager
+
+
+
+GO_DATA_URL = 'https://bio2vec.net/data/mowl/go_subsumption.tar.gz'
+FOODON_DATA_URL = 'https://bio2vec.net/data/mowl/foodon_subsumption.tar.gz'
+
+@versionadded(version='1.0.0')
+class SubsumptionDataset(RemoteDataset):
+    """
+    Dataset for subsumption reasoning tasts of axioms :math:`A \sqsubseteq B` where :math:`A` and :math:`B` are concept names.
+    """
+
+    def __init__(self, url):
+        super().__init__(url)
+
+        self.dataset_dir = os.path.basename(self.ontology_path)
+        self.deductive_closure_ontology_path = os.path.join(self.dataset_dir,
+                                                            "ontology_deductive_closure.owl")
+        self._deductive_closure_ontology = None
+
+    @property
+    def deductive_closure_ontology(self):
+        if self._deductive_closure_ontology is None:
+            ont_manager = OWLManager.createOWLOntologyManager()
+            ontology = ont_manager.loadOntologyFromOntologyDocument(
+                java.io.File(self.deductive_closure_ontology_path))
+            self._deductive_closure_ontology = ontology
+
+        return self._deductive_closure_ontology
+
+
+    # @property
+    # def deductive_closure_ontology(self):
+        # if self._deductive_closure_ontology is None:
+            # self._deductive_closure_ontology = PathDataset(self.root_dir + "train_deductive_closure.owl").ontology
+
+        # return self._deductive_closure_ontology
+
+    @property
+    def evaluation_classes(self):
+        if self._evaluation_classes is None:
+
+            train_classes = self.ontology.getClassesInSignature()
+            valid_classes = self.validation.getClassesInSignature()
+            test_classes = self.testing.getClassesInSignature()
+            deductive_closure_classes = self.deductive_closure_ontology.getClassesInSignature()
+            assert set(valid_classes) - set(train_classes) == set(), f"Valid classes not in train: {set(valid_classes) - set(train_classes)}"
+            assert set(test_classes) - set(train_classes) == set(), f"Test classes not in train: {set(test_classes) - set(train_classes)}"
+            assert set(deductive_closure_classes) - set(train_classes) == set(), f"Deductive closure classes not in train: {set(deductive_closure_classes) - set(train_classes)}"
+
+            classes = self.ontology.getClassesInSignature()
+
+            bot_in_classes = False
+            top_in_classes = False
+
+            for cls in classes:
+                if cls.isOWLNothing():
+                    bot_in_classes = True
+                    continue
+                if cls.isOWLThing():
+                    top_in_classes = True
+                    continue
+
+            if not bot_in_classes:
+                print("Did not find owl:Nothing in ontology classes. Adding it")
+                classes.add(self.ontology.getOWLOntologyManager().getOWLDataFactory().getOWLNothing())
+            if not top_in_classes:
+                print("Did not find owl:Thing in classes. Adding it")
+                classes.add(self.ontology.getOWLOntologyManager().getOWLDataFactory().getOWLThing())
+
+            classes = OWLClasses(classes)
+            self._evaluation_classes = classes, classes
+
+        return self._evaluation_classes
+
+
+class GOSubsumptionDataset(SubsumptionDataset):
+    """
+    Dataset for subsumption prediction in the Gene Ontology. Axioms to be predicted are of the form :math:`A \sqsubseteq B` where :math:`A` and :math:`B` are GO terms. This dataset is based on [chen2020b]_.
+    """
+    def __init__(self):
+        super().__init__(GO_DATA_URL)
+
+
+class FoodOnSubsumptionDataset(SubsumptionDataset):
+    """
+    Dataset for subsumption prediction in the Gene Ontology. Axioms to be predicted are of the form :math:`A \sqsubseteq B` where :math:`A` and :math:`B` are GO terms. This dataset is based on [chen2020b]_.
+    """
+    def __init__(self):
+        super().__init__(FOODON_DATA_URL)