From 224953b8e30329d35a3d29b5800e28ff596a8cb5 Mon Sep 17 00:00:00 2001 From: Shalsh Date: Thu, 26 Mar 2020 20:58:01 -0400 Subject: [PATCH] Include term superclasses relations in kb --- src/main/scala/org/phenoscape/owl/build/PhenoscapeKB.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/scala/org/phenoscape/owl/build/PhenoscapeKB.scala b/src/main/scala/org/phenoscape/owl/build/PhenoscapeKB.scala index c757004..95cf235 100644 --- 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()