updated TTO import

Author: cmllezr

src/ontology/distel-mech.Makefile

@@ -11,8 +11,34 @@ PMDCO_CLASSES_TO_REMOVE = $(IMPORTDIR)/pmdco_classes_to_remove.txt
 
 
 # Import TTO classes preserving subclass hierarchy to PMDco
-$(IMPORTDIR)/tto_import.owl: $(MIRRORDIR)/tto.owl $(IMPORTDIR)/tto_terms.txt $(IMPORTSEED) | all_robot_plugins
+#$(IMPORTDIR)/tto_import.owl: $(MIRRORDIR)/tto.owl $(IMPORTDIR)/tto_terms.txt $(IMPORTSEED) | all_robot_plugins
+#
+#	$(ROBOT) annotate --input $< --remove-annotations \
+#			odk:normalize --add-source true \
+#			extract --term-file $(IMPORTDIR)/tto_terms.txt \
+#						--force true \
+#						--copy-ontology-annotations true \
+#						--individuals exclude \
+#						--intermediates all \
+#						--method BOT \
+#			remove --term-file $(IMPORTDIR)/tto_remove_parent.txt \
+#					--select "ancestors" \
+#					--trim false \
+#			remove --select "complement" --select "named" --trim true \
+#			remove --term-file $(IAO_TO_REMOVE) \
+#				   --select "individuals classes"\
+#			remove --term-file $(IMPORTDIR)/tto_to_remove.txt \
+#				   --select "classes"\
+#			remove --select individuals \
+#			odk:normalize --base-iri https://w3id.org/pmd/distel \
+#							--subset-decls true --synonym-decls true \
+#			remove --term http://purl.obolibrary.org/obo/IAO_0000412 \
+#					--select annotation \
+#			annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+#			convert -f owl --output $@.tmp.owl && mv $@.tmp.owl $@
 
+$(IMPORTDIR)/tto_import.owl: $(MIRRORDIR)/tto.owl $(IMPORTDIR)/tto_terms.txt $(IMPORTSEED) | all_robot_plugins
+	@echo "Generating import module from private TTO mirror..."
 	$(ROBOT) annotate --input $< --remove-annotations \
 			odk:normalize --add-source true \
 			extract --term-file $(IMPORTDIR)/tto_terms.txt \
@@ -21,23 +47,15 @@ $(IMPORTDIR)/tto_import.owl: $(MIRRORDIR)/tto.owl $(IMPORTDIR)/tto_terms.txt $(I
 						--individuals exclude \
 						--intermediates all \
 						--method BOT \
-			remove --term-file $(IMPORTDIR)/tto_remove_parent.txt \
-					--select "ancestors" \
-					--trim false \
-			remove --select "complement" --select "named" --trim true \
-			remove --term-file $(IAO_TO_REMOVE) \
-				   --select "individuals classes"\
-			remove --term-file $(IMPORTDIR)/tto_to_remove.txt \
-				   --select "classes"\
-			remove --select individuals \
+			remove --term "https://w3id.org/pmd/co/relatesTo" \
+				   -- select "self" \
+				   --axioms "logical" \
+				   --trim true \
 			odk:normalize --base-iri https://w3id.org/pmd/distel \
 							--subset-decls true --synonym-decls true \
-			remove --term http://purl.obolibrary.org/obo/IAO_0000412 \
-					--select annotation \
 			annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 			convert -f owl --output $@.tmp.owl && mv $@.tmp.owl $@
 
-
 $(IMPORTDIR)/pmdco_import.owl: $(MIRRORDIR)/pmdco.owl $(IMPORTDIR)/pmdco_terms.txt
 	@echo "Generating Application Module from pmdco..."
 	if [ $(IMP) = true ]; then $(ROBOT) \