diff --git a/Makefile b/Makefile
index 214119d38..9a3afbab2 100644
--- a/Makefile
+++ b/Makefile
@@ -273,7 +273,7 @@ publish: $(DO).owl $(DO).obo $(DO).json\
 post: build/reports/report-diff.txt build/reports/branch-count.tsv build/reports/removed-axioms.html
 
 # Get the last build of DO from IRI
-.PHONY: build/doid-last.owl
+#.PHONY: build/doid-last.owl
 build/doid-last.owl: | build/robot.jar
 	@$(ROBOT) merge \
 	 --input-iri http://purl.obolibrary.org/obo/doid/doid-merged.owl \
@@ -285,8 +285,9 @@ QUERIES := $(wildcard src/sparql/*-report.rq)
 
 # target names for previous release reports
 LAST_REPORTS := $(foreach Q,$(QUERIES), $(subst src/sparql,build/reports,$(subst .rq,-last.tsv,$(Q))))
-.PHONY: $(LAST_REPORTS)
-build/reports/%-last.tsv: src/sparql/%-report.rq build/doid-last.owl | build/reports
+.PHONY: last-reports
+last-reports: $(LAST_REPORTS)
+build/reports/%-last.tsv: src/sparql/%.rq build/doid-last.owl | build/reports
 	@echo "Counting: $(notdir $(basename $@))"
 	@$(ROBOT) query \
 	 --input $(word 2,$^) \
@@ -294,18 +295,21 @@ build/reports/%-last.tsv: src/sparql/%-report.rq build/doid-last.owl | build/rep
 
 # target names for current release reports
 NEW_REPORTS := $(foreach Q,$(QUERIES), $(subst src/sparql,build/reports,$(subst .rq,-new.tsv,$(Q))))
-.PHONY: $(NEW_REPORTS)
-build/reports/%-new.tsv: src/sparql/%-report.rq $(DM).owl | build/reports
+.PHONY: new-reports
+new-reports: $(NEW_REPORTS)
+build/reports/%-new.tsv: src/sparql/%.rq $(DM).owl | build/reports
 	@echo "Counting: $(notdir $(basename $@))"
 	@$(ROBOT) query \
 	 --input $(word 2,$^) \
 	 --query $< $@
 
-build/reports/report-diff.txt: $(LAST_REPORTS) $(NEW_REPORTS)
+# create a clean diff between last and current reports
+build/reports/report-diff.txt: last-reports new-reports
 	@python src/util/report-diff.py
 	@mv $@ $(DIR)/report-diff.txt
 	@echo "Release diff report available at $(DIR)/report-diff.txt"
 
+# create a count of the various disease branches
 .PHONY: build/reports/branch-count.tsv
 build/reports/branch-count.tsv: $(DNC).owl | build/robot.jar build/reports
 	@echo "Counting all branches..."
diff --git a/src/ontology/releases/2019-09-16/report-diff.txt b/src/ontology/releases/2019-09-16/report-diff.txt
index 8864d1591..4287bf675 100644
--- a/src/ontology/releases/2019-09-16/report-diff.txt
+++ b/src/ontology/releases/2019-09-16/report-diff.txt
@@ -1,27 +1,27 @@
 RELEASE DIFF REPORT
 
 XREF-REPORT
-	omim		+0
-	mesh		+0
-	nci			+0
+	omim		--43
+	mesh		--2
+	nci			--2457
 
 IMPORT-REPORT
 	uberon		+0
 	so			+0
 	ncbi		+0
-	symp		+0
-	hp			+0
+	symp		+1
+	hp			+2
 	foodon		+0
 	cl			+0
 	chebi		+0
 	trans		+0
 
 DOID-REPORT
-	classes		+0
+	classes		+26
 
 DEF-REPORT
-	classes		+0
+	classes		+28
 
 LOGICAL-DEFINITIONS-REPORT
-	equivalent	+0
-	subClassOf	+0
+	equivalent	--1
+	subClassOf	+92
diff --git a/src/sparql/doid-report.rq b/src/sparql/doid-report.rq
index 05544547b..a8ce37bf7 100644
--- a/src/sparql/doid-report.rq
+++ b/src/sparql/doid-report.rq
@@ -5,5 +5,5 @@ PREFIX owl: <http://www.w3.org/2002/07/owl#>
 SELECT (COUNT(?s) AS ?classes) WHERE {
 	?s a owl:Class .
 	FILTER STRSTARTS(str(?s), "http://purl.obolibrary.org/obo/DOID_")
-	FILTER NOT EXISTS {?s owl:deprecated "true"}
+	FILTER NOT EXISTS {?s owl:deprecated ?any}
 }
\ No newline at end of file