Merge pull request #631 from monarch-initiative/add-baseplus

Add baseplus release and update QC to complain with equivalents

src/ontology/Makefile

@@ -85,7 +85,7 @@ release_diff: $(REPORTDIR)/release-diff.md
 
 .PHONY: reason_test
 reason_test: $(EDIT_PREPROCESSED)
-	$(ROBOT) reason --input $< --reasoner ELK --equivalent-classes-allowed all \
+	$(ROBOT) reason --input $< --reasoner ELK --equivalent-classes-allowed asserted-only \
 		--exclude-tautologies structural --output test.owl && rm test.owl
 
 .PHONY: odkversion
@@ -762,7 +762,7 @@ $(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC)
 # Full: The full artefacts with imports merged, reasoned.
 $(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
 	$(ROBOT_RELEASE_IMPORT_MODE) \
-		reason --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural \
+		reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
 		relax \
 		reduce -r ELK \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@

src/ontology/maxo-odk.yaml

@@ -88,7 +88,7 @@ components:
       use_template: TRUE
       templates:
         - maxo-in-progress.tsv
-allow_equivalents: all
+allow_equivalents: asserted-only
 robot_report:
   use_base_iris: True
   fail_on : ERROR

src/ontology/maxo.Makefile

@@ -15,6 +15,17 @@ test: maxo-base.json
 test_fast:
 	$(MAKE_FAST) test
 
+$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
+	$(ROBOT_RELEASE_IMPORT_MODE) \
+	reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
+	relax \
+	reduce -r ELK \
+	remove --base-iri $(URIBASE)/MAXO_ --axioms external --preserve-structure false --trim false \
+	$(SHARED_ROBOT_COMMANDS) \
+	annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \
+		--ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
+		--output $@.tmp.owl && mv $@.tmp.owl $@
+
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 ### Generating all ROBOT templates ######
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