Merge pull request #57 from phenoscape/term-superclasses

Include term superclasses relations in kb
phenoscape · Mar 27, 2020 · 8bab2aa · 8bab2aa
2 parents 645bad1 + 224953b
commit 8bab2aa
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/main/scala/org/phenoscape/owl/build/PhenoscapeKB.scala b/src/main/scala/org/phenoscape/owl/build/PhenoscapeKB.scala
@@ -153,7 +153,7 @@ object PhenoscapeKB extends KnowledgeBaseBuilder {
 
     step("Querying entities and qualities")
     val coreReasoner = reasoner(Set(uberon, cl, pato, bspo, phenoscapeVocab).flatMap(_.axioms))
-    val anatomicalEntities = coreReasoner.getSubClasses(Class(Vocab.ANATOMICAL_ENTITY), false).getFlattened.asScala.filterNot(_.isOWLNothing) + Class(Vocab.ANATOMICAL_ENTITY)
+    val anatomicalEntities = coreReasoner.getSubClasses(Class(Vocab.ANATOMICAL_ENTITY), false).getFlattened.asScala.filterNot(_.isOWLNothing) ++ coreReasoner.getSuperClasses(Class(Vocab.ANATOMICAL_ENTITY), false).getFlattened.asScala.filterNot(_.isOWLThing) + Class(Vocab.ANATOMICAL_ENTITY)
     val qualities = coreReasoner.getSubClasses(Class(Vocab.QUALITY), false).getFlattened.asScala.filterNot(_.isOWLNothing) + Class(Vocab.QUALITY)
     coreReasoner.dispose()