diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
index 3502f1c..268f5be 100644
--- a/.github/workflows/qc.yml
+++ b/.github/workflows/qc.yml
@@ -5,10 +5,10 @@ name: CI
 # Controls when the action will run. 
 on:
   # Triggers the workflow on push or pull request events but only for the main branch
-  #push:
-  #  branches: [ main ]
-  #pull_request:
-  #  branches: [ main ]
+  # push:
+  #   branches: [ main ]
+  # pull_request:
+  #   branches: [ main ]
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -19,15 +19,15 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.3.0
+    container: obolibrary/odkfull:v1.5
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Run ontology QC checks
         env:
           DEFAULT_BRANCH: main
-        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false
 
diff --git a/docs/odk-workflows/ManageDocumentation.md b/docs/odk-workflows/ManageDocumentation.md
index 1dd2809..da52d77 100644
--- a/docs/odk-workflows/ManageDocumentation.md
+++ b/docs/odk-workflows/ManageDocumentation.md
@@ -44,3 +44,4 @@ The documentation is _not_ automatically updated from the Markdown, and needs to
    Just make sure you give GitHub 2-5 minutes to build the pages!
 
 
+
diff --git a/docs/odk-workflows/RepoManagement.md b/docs/odk-workflows/RepoManagement.md
index 724badb..8f2eb1f 100644
--- a/docs/odk-workflows/RepoManagement.md
+++ b/docs/odk-workflows/RepoManagement.md
@@ -2,7 +2,7 @@
 
 ## Updating your ODK repository
 
-Your ODK repositories configuration is managed in `src/ontology/phenio-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository:
+Your ODK repositories configuration is managed in `src/ontology/phenio-odk.yaml`. The [ODK Project Configuration Schema](https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md) defines all possible parameters that can be used in this config YAML. Once you have made your changes, you can run the following to apply your changes to the repository:
 
 
 ```
diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md
index 6c9b6ef..137f938 100644
--- a/docs/odk-workflows/RepositoryFileStructure.md
+++ b/docs/odk-workflows/RepositoryFileStructure.md
@@ -46,6 +46,7 @@ These are the components in PHENIO
 | Filename | URL |
 | -------- | --- |
 | bfo.owl | http://purl.obolibrary.org/obo/bfo.owl |
+| ddpheno.owl | http://purl.obolibrary.org/obo/ddpheno.owl |
 | emapa.owl | http://purl.obolibrary.org/obo/emapa.owl |
 | fbbt.owl | http://purl.obolibrary.org/obo/fbbt.owl |
 | go.owl | http://purl.obolibrary.org/obo/go.owl |
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
index c310372..9fa8b42 100644
--- a/src/ontology/Makefile
+++ b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for phenio
 # Generated using ontology-development-kit
-# ODK Version: v1.4.3
+# ODK Version: v1.5
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use phenio.Makefile instead
 
@@ -9,6 +9,9 @@
 # ----------------------------------------
 # More information: https://github.com/INCATools/ontology-development-kit/
 
+# Fingerprint of the configuration file when this Makefile was last generated
+CONFIG_HASH=                1126eedd8e58276f7dc4423f54c5463ff19cc8d1c79755b1eb65763cea44fb0f
+
 
 # ----------------------------------------
 # Standard Constants
@@ -43,14 +46,14 @@ REPORT_PROFILE_OPTS =
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by 
 SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.4.3
+ODK_VERSION_MAKEFILE =      v1.5
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
-OTHER_SRC =                 $(COMPONENTSDIR)/bfo.owl $(COMPONENTSDIR)/emapa.owl $(COMPONENTSDIR)/fbbt.owl $(COMPONENTSDIR)/go.owl $(COMPONENTSDIR)/hsapdv.owl $(COMPONENTSDIR)/mondo.owl $(COMPONENTSDIR)/mpath.owl $(COMPONENTSDIR)/nbo.owl $(COMPONENTSDIR)/ro.owl $(COMPONENTSDIR)/uberon.owl $(COMPONENTSDIR)/upheno.owl $(COMPONENTSDIR)/wbbt.owl $(COMPONENTSDIR)/zfa.owl 
+OTHER_SRC =                 $(COMPONENTSDIR)/bfo.owl $(COMPONENTSDIR)/ddpheno.owl $(COMPONENTSDIR)/emapa.owl $(COMPONENTSDIR)/fbbt.owl $(COMPONENTSDIR)/go.owl $(COMPONENTSDIR)/hsapdv.owl $(COMPONENTSDIR)/mondo.owl $(COMPONENTSDIR)/mpath.owl $(COMPONENTSDIR)/nbo.owl $(COMPONENTSDIR)/ro.owl $(COMPONENTSDIR)/uberon.owl $(COMPONENTSDIR)/upheno.owl $(COMPONENTSDIR)/wbbt.owl $(COMPONENTSDIR)/zfa.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 
@@ -58,6 +61,11 @@ FORMATS = $(sort  owl json owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
 RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full )
 
+ifeq ($(ODK_DEBUG),yes)
+ODK_DEBUG_FILE = debug.log
+SHELL = $(SCRIPTSDIR)/run-command.sh
+endif
+
 # ----------------------------------------
 # Top-level targets
 # ----------------------------------------
@@ -68,12 +76,16 @@ RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full )
 all: all_odk
 
 .PHONY: all_odk
-all_odk: odkversion test all_assets
+all_odk: odkversion config_check test custom_reports all_assets
 
 .PHONY: test
 test: odkversion reason_test sparql_test robot_reports 
 	echo "Finished running all tests successfully."
 
+.PHONY: test
+test_fast:
+	$(MAKE_FAST) test
+
 .PHONY: release_diff
 release_diff: $(REPORTDIR)/release-diff.md
 
@@ -84,13 +96,52 @@ reason_test: $(EDIT_PREPROCESSED)
 
 .PHONY: odkversion
 odkversion:
-	echo "ODK Makefile version: $(ODK_VERSION_MAKEFILE) (this is the version of the ODK with which this Makefile was generated, \
-        not the version of the ODK you are running)" &&\
-	echo "ROBOT version (ODK): " && $(ROBOT) --version
+	@echo "ODK Makefile $(ODK_VERSION_MAKEFILE)"
+	@odk-info --tools
+.PHONY: config_check
+config_check:
+	@if [ "$$(sha256sum $(ONT)-odk.yaml | cut -c1-64)" = "$(CONFIG_HASH)" ]; then \
+		echo "Repository is up-to-date." ; else \
+		echo "Your ODK configuration has changed since this Makefile was generated. You may need to run 'make update_repo'." ; fi
+
 
 $(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR):
 	mkdir -p $@
 
+# ----------------------------------------
+# ODK-managed ROBOT plugins
+# ----------------------------------------
+
+# Make sure ROBOT knows where to find plugins
+export ROBOT_PLUGINS_DIRECTORY=$(TMPDIR)/plugins
+
+# Override this rule in phenio.Makefile to install custom plugins
+.PHONY: custom_robot_plugins
+custom_robot_plugins:
+
+
+.PHONY: extra_robot_plugins
+extra_robot_plugins: 
+
+
+# Install all ROBOT plugins to the runtime plugins directory
+.PHONY: all_robot_plugins
+all_robot_plugins: $(foreach plugin,$(notdir $(wildcard /tools/robot-plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \
+		   $(foreach plugin,$(notdir $(wildcard ../../plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \
+		   custom_robot_plugins extra_robot_plugins  \
+
+# Default rule to install plugins
+$(ROBOT_PLUGINS_DIRECTORY)/%.jar:
+	@mkdir -p $(ROBOT_PLUGINS_DIRECTORY)
+	@if [ -f ../../plugins/$*.jar ]; then        \
+		ln ../../plugins/$*.jar $@ ;         \
+	elif [ -f /tools/robot-plugins/$*.jar ]; then \
+		cp /tools/robot-plugins/$*.jar $@ ;  \
+	fi
+
+# Specific rules for supplementary plugins defined in configuration
+
+
 # ----------------------------------------
 # Release assets
 # ----------------------------------------
@@ -180,10 +231,10 @@ validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt
 
 SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql)
 
-sparql_test:  $(EDIT_PREPROCESSED) catalog-v001.xml | $(REPORTDIR)
+sparql_test:  $(EDIT_PREPROCESSED) | $(REPORTDIR)
 ifneq ($(SPARQL_VALIDATION_QUERIES),)
   
-	$(ROBOT) verify  --catalog catalog-v001.xml -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
+	$(ROBOT) verify -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
 endif
 
 # ----------------------------------------
@@ -196,6 +247,10 @@ $(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR)
 $(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR)
 	$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
 
+check_for_robot_updates:
+	echo "You are not using a custom profile, so you are getting the joy of the latest ROBOT report!"
+
+
 # ----------------------------------------
 # Release assets
 # ----------------------------------------
@@ -213,7 +268,7 @@ RELEASE_ASSETS = \
   $(REPORT_FILES)
 
 .PHONY: all_assets
-all_assets: $(ASSETS) 
+all_assets: $(ASSETS) check_rdfxml_assets
 
 .PHONY: show_assets
 show_assets:
@@ -221,7 +276,7 @@ show_assets:
 	du -sh $(ASSETS)
 
 check_rdfxml_%: %
-	@check-rdfxml $<
+	@check-rdfxml  $<
 
 .PHONY: check_rdfxml_assets
 check_rdfxml_assets: $(foreach product,$(MAIN_PRODUCTS),check_rdfxml_$(product).owl)
@@ -309,6 +364,7 @@ $(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_term
 	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
 		remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://purl.obolibrary.org/obo/NCBITaxon_Union_*>" remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/OBA_*>" remove  --select "<http://purl.obolibrary.org/obo/CARO_*>"  \
 		extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
+		remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/merged_terms_combined.txt --select complement --select annotation-properties \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \
 		$(ANNOTATE_CONVERT_FILE); fi
 
@@ -378,9 +434,9 @@ recreate-%:
 no-mirror-recreate-%:
 	$(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=false PAT=true $(COMPONENTSDIR)/$*.owl -B
 
-$(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
-	touch $@
-.PRECIOUS: $(COMPONENTSDIR)/%
+$(COMPONENTSDIR)/%.owl: | $(COMPONENTSDIR)
+	test -f $@ || touch $@
+.PRECIOUS: $(COMPONENTSDIR)/%.owl
 
 
 
@@ -389,20 +445,41 @@ component-download-bfo.owl: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I http://purl.obolibrary.org/obo/bfo.owl \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/bfo.owl:  component-download-bfo.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-bfo.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-bfo.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/bfo.owl: component-download-bfo.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-bfo.owl.owl $(TMPDIR)/component-download-bfo.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-bfo.owl.owl $(TMPDIR)/component-download-bfo.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-bfo.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/bfo.owl
 
 
+.PHONY: component-download-ddpheno.owl
+component-download-ddpheno.owl: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I http://purl.obolibrary.org/obo/ddpheno.owl \
+	remove --base-iri http://purl.obolibrary.org/obo/ddpheno# --base-iri http://purl.obolibrary.org/obo/DDPHENO_ --axioms external --preserve-structure false --trim false \
+	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
+
+$(COMPONENTSDIR)/ddpheno.owl: component-download-ddpheno.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-ddpheno.owl.owl $(TMPDIR)/component-download-ddpheno.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-ddpheno.owl.owl $(TMPDIR)/component-download-ddpheno.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-ddpheno.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
+
+.PRECIOUS: $(COMPONENTSDIR)/ddpheno.owl
+
+
 .PHONY: component-download-emapa.owl
 component-download-emapa.owl: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I http://purl.obolibrary.org/obo/emapa.owl \
 	remove --base-iri http://purl.obolibrary.org/obo/emapa# --base-iri http://purl.obolibrary.org/obo/EMAPA_ --axioms external --preserve-structure false --trim false \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/emapa.owl:  component-download-emapa.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-emapa.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-emapa.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/emapa.owl: component-download-emapa.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-emapa.owl.owl $(TMPDIR)/component-download-emapa.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-emapa.owl.owl $(TMPDIR)/component-download-emapa.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-emapa.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/emapa.owl
 
@@ -413,8 +490,11 @@ component-download-fbbt.owl: | $(TMPDIR)
 	remove --base-iri http://purl.obolibrary.org/obo/fbbt# --base-iri http://purl.obolibrary.org/obo/FBbt_ --axioms external --preserve-structure false --trim false \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/fbbt.owl:  component-download-fbbt.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-fbbt.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-fbbt.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/fbbt.owl: component-download-fbbt.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-fbbt.owl.owl $(TMPDIR)/component-download-fbbt.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-fbbt.owl.owl $(TMPDIR)/component-download-fbbt.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-fbbt.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/fbbt.owl
 
@@ -425,8 +505,11 @@ component-download-go.owl: | $(TMPDIR)
 	remove --base-iri http://purl.obolibrary.org/obo/go# --base-iri http://purl.obolibrary.org/obo/GO_ --axioms external --preserve-structure false --trim false \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/go.owl:  component-download-go.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-go.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-go.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/go.owl: component-download-go.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-go.owl.owl $(TMPDIR)/component-download-go.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-go.owl.owl $(TMPDIR)/component-download-go.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-go.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/go.owl
 
@@ -437,8 +520,11 @@ component-download-hsapdv.owl: | $(TMPDIR)
 	remove --base-iri http://purl.obolibrary.org/obo/hsapdv# --base-iri http://purl.obolibrary.org/obo/HsapDv_ --axioms external --preserve-structure false --trim false \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/hsapdv.owl:  component-download-hsapdv.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-hsapdv.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-hsapdv.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/hsapdv.owl: component-download-hsapdv.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-hsapdv.owl.owl $(TMPDIR)/component-download-hsapdv.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-hsapdv.owl.owl $(TMPDIR)/component-download-hsapdv.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-hsapdv.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/hsapdv.owl
 
@@ -449,8 +535,11 @@ component-download-mondo.owl: | $(TMPDIR)
 	remove --base-iri http://purl.obolibrary.org/obo/mondo# --base-iri http://purl.obolibrary.org/obo/MONDO_ --axioms external --preserve-structure false --trim false \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/mondo.owl:  component-download-mondo.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-mondo.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-mondo.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/mondo.owl: component-download-mondo.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-mondo.owl.owl $(TMPDIR)/component-download-mondo.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-mondo.owl.owl $(TMPDIR)/component-download-mondo.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-mondo.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/mondo.owl
 
@@ -461,8 +550,11 @@ component-download-mpath.owl: | $(TMPDIR)
 	remove --base-iri http://purl.obolibrary.org/obo/mpath# --base-iri http://purl.obolibrary.org/obo/MPATH_ --axioms external --preserve-structure false --trim false \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/mpath.owl:  component-download-mpath.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-mpath.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-mpath.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/mpath.owl: component-download-mpath.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-mpath.owl.owl $(TMPDIR)/component-download-mpath.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-mpath.owl.owl $(TMPDIR)/component-download-mpath.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-mpath.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/mpath.owl
 
@@ -473,8 +565,11 @@ component-download-nbo.owl: | $(TMPDIR)
 	remove --base-iri http://purl.obolibrary.org/obo/nbo.owl# --base-iri http://purl.obolibrary.org/obo/NBO_ --axioms external --preserve-structure false --trim false \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/nbo.owl:  component-download-nbo.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-nbo.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-nbo.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/nbo.owl: component-download-nbo.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-nbo.owl.owl $(TMPDIR)/component-download-nbo.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-nbo.owl.owl $(TMPDIR)/component-download-nbo.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-nbo.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/nbo.owl
 
@@ -484,8 +579,11 @@ component-download-ro.owl: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I http://purl.obolibrary.org/obo/ro.owl \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/ro.owl:  component-download-ro.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-ro.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-ro.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/ro.owl: component-download-ro.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-ro.owl.owl $(TMPDIR)/component-download-ro.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-ro.owl.owl $(TMPDIR)/component-download-ro.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-ro.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/ro.owl
 
@@ -496,8 +594,11 @@ component-download-uberon.owl: | $(TMPDIR)
 	remove --base-iri http://purl.obolibrary.org/obo/UBERON_ --base-iri http://purl.obolibrary.org/obo/uberon/core# --base-iri http://purl.obolibrary.org/obo/UBPROP_ --axioms external --preserve-structure false --trim false \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/uberon.owl:  component-download-uberon.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-uberon.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-uberon.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/uberon.owl: component-download-uberon.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-uberon.owl.owl $(TMPDIR)/component-download-uberon.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-uberon.owl.owl $(TMPDIR)/component-download-uberon.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-uberon.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/uberon.owl
 
@@ -508,8 +609,11 @@ component-download-upheno.owl: | $(TMPDIR)
 	remove --base-iri http://purl.obolibrary.org/obo/UPHENO_ --base-iri http://purl.obolibrary.org/obo/HP_ --base-iri http://purl.obolibrary.org/obo/MP_ --base-iri http://purl.obolibrary.org/obo/WBPhenotype_ --base-iri http://purl.obolibrary.org/obo/XPO_ --base-iri http://purl.obolibrary.org/obo/ZP_ --base-iri http://purl.obolibrary.org/obo/FYPO_ --axioms external --preserve-structure false --trim false \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/upheno.owl:  component-download-upheno.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-upheno.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-upheno.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/upheno.owl: component-download-upheno.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-upheno.owl.owl $(TMPDIR)/component-download-upheno.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-upheno.owl.owl $(TMPDIR)/component-download-upheno.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-upheno.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/upheno.owl
 
@@ -520,8 +624,11 @@ component-download-wbbt.owl: | $(TMPDIR)
 	remove --base-iri http://purl.obolibrary.org/obo/wbbt# --base-iri http://purl.obolibrary.org/obo/WBbt_ --axioms external --preserve-structure false --trim false \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/wbbt.owl:  component-download-wbbt.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-wbbt.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-wbbt.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/wbbt.owl: component-download-wbbt.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-wbbt.owl.owl $(TMPDIR)/component-download-wbbt.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-wbbt.owl.owl $(TMPDIR)/component-download-wbbt.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-wbbt.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/wbbt.owl
 
@@ -532,8 +639,11 @@ component-download-zfa.owl: | $(TMPDIR)
 	remove --base-iri http://purl.obolibrary.org/obo/zfa# --base-iri http://purl.obolibrary.org/obo/ZFA_ --axioms external --preserve-structure false --trim false \
 	annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi
 
-$(COMPONENTSDIR)/zfa.owl:  component-download-zfa.owl
-	if [ $(COMP) = true ] ; then if cmp -s $(TMPDIR)/component-download-zfa.owl.owl $@ ; then echo "Component identical."; else echo "Component is different, updating." && cp $(TMPDIR)/component-download-zfa.owl.owl $@; fi; fi
+$(COMPONENTSDIR)/zfa.owl: component-download-zfa.owl
+	if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-zfa.owl.owl $(TMPDIR)/component-download-zfa.owl.tmp.owl ; then echo "Component identical."; \
+      else echo "Component is different, updating." &&\
+		cp $(TMPDIR)/component-download-zfa.owl.owl $(TMPDIR)/component-download-zfa.owl.tmp.owl &&\
+		$(ROBOT) annotate -i $(TMPDIR)/component-download-zfa.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi
 
 .PRECIOUS: $(COMPONENTSDIR)/zfa.owl
 # ----------------------------------------
@@ -544,160 +654,154 @@ IMP=true # Global parameter to bypass import generation
 MIR=true # Global parameter to bypass mirror generation
 IMP_LARGE=true # Global parameter to bypass handling of large imports
 
+ifeq ($(strip $(MIR)),true)
 
 
 ## ONTOLOGY: chebi
 .PHONY: mirror-chebi
 .PRECIOUS: $(MIRRORDIR)/chebi.owl
+ifeq ($(strip $(IMP_LARGE)),true)
 mirror-chebi: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then curl -L $(OBOBASE)/chebi.owl.gz --create-dirs -o $(MIRRORDIR)/chebi.owl.gz --retry 4 --max-time 400 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/chebi.owl.gz -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/chebi.owl.gz --create-dirs -o $(MIRRORDIR)/chebi.owl.gz --retry 4 --max-time 400 && \
+	$(ROBOT) convert -i $(MIRRORDIR)/chebi.owl.gz -o $(TMPDIR)/$@.owl
+else
+mirror-chebi:
+	@echo "Not refreshing chebi because refreshing large imports is disabled (IMP_LARGE=$(IMP_LARGE))."
+endif
 
 
 ## ONTOLOGY: eco
 .PHONY: mirror-eco
 .PRECIOUS: $(MIRRORDIR)/eco.owl
 mirror-eco: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/eco.owl --create-dirs -o $(MIRRORDIR)/eco.owl --retry 4 --max-time 400 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/eco.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/ECO --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/eco.owl --create-dirs -o $(TMPDIR)/eco-download.owl --retry 4 --max-time 400 && \
+	$(ROBOT) remove -i $(TMPDIR)/eco-download.owl --base-iri $(OBOBASE)/ECO --axioms external --preserve-structure false --trim false -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: ncbitaxon-taxslim
 .PHONY: mirror-ncbitaxon-taxslim
 .PRECIOUS: $(MIRRORDIR)/ncbitaxon-taxslim.owl
 mirror-ncbitaxon-taxslim: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: oba
 .PHONY: mirror-oba
 .PRECIOUS: $(MIRRORDIR)/oba.owl
 mirror-oba: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/oba.owl --create-dirs -o $(MIRRORDIR)/oba.owl --retry 4 --max-time 400 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/oba.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/oba.owl --create-dirs -o $(TMPDIR)/oba-download.owl --retry 4 --max-time 400 && \
+	$(ROBOT) convert -i $(TMPDIR)/oba-download.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: pato
 .PHONY: mirror-pato
 .PRECIOUS: $(MIRRORDIR)/pato.owl
 mirror-pato: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pato.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 400 &&\
-		$(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	curl -L $(OBOBASE)/pato.owl --create-dirs -o $(TMPDIR)/pato-download.owl --retry 4 --max-time 400 && \
+	$(ROBOT) convert -i $(TMPDIR)/pato-download.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: uberon-bridge-to-emapa
 .PHONY: mirror-uberon-bridge-to-emapa
 .PRECIOUS: $(MIRRORDIR)/uberon-bridge-to-emapa.owl
 mirror-uberon-bridge-to-emapa: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-emapa.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-emapa.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: uberon-bridge-to-zfa
 .PHONY: mirror-uberon-bridge-to-zfa
 .PRECIOUS: $(MIRRORDIR)/uberon-bridge-to-zfa.owl
 mirror-uberon-bridge-to-zfa: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-zfa.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: uberon-bridge-to-ma
 .PHONY: mirror-uberon-bridge-to-ma
 .PRECIOUS: $(MIRRORDIR)/uberon-bridge-to-ma.owl
 mirror-uberon-bridge-to-ma: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-ma.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: uberon-bridge-to-wbbt
 .PHONY: mirror-uberon-bridge-to-wbbt
 .PRECIOUS: $(MIRRORDIR)/uberon-bridge-to-wbbt.owl
 mirror-uberon-bridge-to-wbbt: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: uberon-bridge-to-fbbt
 .PHONY: mirror-uberon-bridge-to-fbbt
 .PRECIOUS: $(MIRRORDIR)/uberon-bridge-to-fbbt.owl
 mirror-uberon-bridge-to-fbbt: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbbt.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbbt.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: uberon-bridge-to-fma
 .PHONY: mirror-uberon-bridge-to-fma
 .PRECIOUS: $(MIRRORDIR)/uberon-bridge-to-fma.owl
 mirror-uberon-bridge-to-fma: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fma.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fma.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: cl-bridge-to-emapa
 .PHONY: mirror-cl-bridge-to-emapa
 .PRECIOUS: $(MIRRORDIR)/cl-bridge-to-emapa.owl
 mirror-cl-bridge-to-emapa: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-emapa.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-emapa.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: cl-bridge-to-ma
 .PHONY: mirror-cl-bridge-to-ma
 .PRECIOUS: $(MIRRORDIR)/cl-bridge-to-ma.owl
 mirror-cl-bridge-to-ma: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ma.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-ma.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: cl-bridge-to-fma
 .PHONY: mirror-cl-bridge-to-fma
 .PRECIOUS: $(MIRRORDIR)/cl-bridge-to-fma.owl
 mirror-cl-bridge-to-fma: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fma.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fma.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: cl-bridge-to-wbbt
 .PHONY: mirror-cl-bridge-to-wbbt
 .PRECIOUS: $(MIRRORDIR)/cl-bridge-to-wbbt.owl
 mirror-cl-bridge-to-wbbt: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-wbbt.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-wbbt.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: cl-bridge-to-fbbt
 .PHONY: mirror-cl-bridge-to-fbbt
 .PRECIOUS: $(MIRRORDIR)/cl-bridge-to-fbbt.owl
 mirror-cl-bridge-to-fbbt: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fbbt.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-fbbt.owl -o $(TMPDIR)/$@.owl
 
 
 ## ONTOLOGY: cl-bridge-to-zfa
 .PHONY: mirror-cl-bridge-to-zfa
 .PRECIOUS: $(MIRRORDIR)/cl-bridge-to-zfa.owl
 mirror-cl-bridge-to-zfa: | $(TMPDIR)
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-zfa.owl -o $@.tmp.owl &&\
-		mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
+	$(ROBOT) convert -I http://purl.obolibrary.org/obo/uberon/bridge/cl-bridge-to-zfa.owl -o $(TMPDIR)/$@.owl
 
 ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
 MERGE_MIRRORS = true
 
+ifeq ($(strip $(MERGE_MIRRORS)),true)
 $(MIRRORDIR)/merged.owl: $(ALL_MIRRORS)
-	if [ $(IMP) = true ] && [ $(MERGE_MIRRORS) = true ]; then $(ROBOT) merge $(patsubst %, -i %, $^) -o $@; fi
+	$(ROBOT) merge $(patsubst %, -i %, $^)  -o $@
 .PRECIOUS: $(MIRRORDIR)/merged.owl
+endif
 
 
 $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
-	if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
+	if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\
 		cp $(TMPDIR)/mirror-$*.owl $@; fi; fi
 
+else # MIR=false
+$(MIRRORDIR)/%.owl:
+	@echo "Not refreshing $@ because the mirrorring pipeline is disabled (MIR=$(MIR))."
+endif
 
 
 
@@ -771,9 +875,13 @@ ROBOT_RELEASE_IMPORT_MODE=$(ROBOT) merge --input $<
 # ROBOT pipeline that removes imports, then merges components. This is for release artefacts that start from "base"
 ROBOT_RELEASE_IMPORT_MODE_BASE=$(ROBOT) remove --input $< --select imports --trim false merge $(patsubst %, -i %, $(OTHER_SRC)) 
 
-# base: All the axioms as they are editted by the editors, excluding reasoning
-$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC)
-	$(ROBOT_RELEASE_IMPORT_MODE_BASE) \
+# base: A version of the ontology that does not include any externally imported axioms.
+$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES)
+	$(ROBOT_RELEASE_IMPORT_MODE) \
+	reason --reasoner ELK --equivalent-classes-allowed all --exclude-tautologies structural --annotate-inferred-axioms False \
+	relax \
+	reduce -r ELK \
+	remove --base-iri $(URIBASE)/PHENIO --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) \
@@ -840,13 +948,16 @@ update_repo:
 update_docs:
 	mkdocs gh-deploy --config-file ../../mkdocs.yaml
 
-# Note to future generations: prepending ./ is a safety measure to ensure that 
-# the environment does not malicously set `CLEANFILES` to `\`.
+# Note to future generations: computing the real path relative to the
+# current directory is a way to ensure we only clean up directories that
+# are located below the current directory, regardless of the contents of
+# the *DIR variables.
 .PHONY: clean
 clean:
-	[ -n "$(MIRRORDIR)" ] && [ $(MIRRORDIR) != "." ] && [ $(MIRRORDIR) != "/" ] && [ $(MIRRORDIR) != ".." ] && [ -d ./$(MIRRORDIR) ] && rm -rf ./$(MIRRORDIR)/*
-	[ -n "$(TMPDIR)" ] && [ $(TMPDIR) != "." ] && [ $(TMPDIR) != "/" ] && [ $(TMPDIR) != ".." ] && [ -d ./$(TMPDIR) ] && rm -rf ./$(TMPDIR)/*
-	[ -n "$(UPDATEREPODIR)" ] && [ $(UPDATEREPODIR) != "." ] && [ $(UPDATEREPODIR) != "/" ] && [ $(UPDATEREPODIR) != ".." ] && [ -d ./$(UPDATEREPODIR) ] && rm -rf ./$(UPDATEREPODIR)/*
+	for dir in $(MIRRORDIR) $(TMPDIR) $(UPDATEREPODIR) ; do      \
+		reldir=$$(realpath --relative-to=$$(pwd) $$dir) ;    \
+		case $$reldir in .*|"") ;; *) rm -rf $$reldir/* ;; esac \
+	done
 	rm -f $(CLEANFILES)
 
 .PHONY: help
@@ -865,6 +976,7 @@ Core commands:
 * prepare_release_fast:	Run the entire release pipeline without refreshing imports, recreating components or recompiling patterns.
 * update_repo:		Update the ODK repository setup using the config file phenio-odk.yaml
 * test:			Running all validation tests
+* test_fast:		Runs the test suite, but without updating imports or components
 * odkversion:		Show the current version of the ODK Makefile and ROBOT.
 * clean:		Delete all temporary files
 * help:			Print ODK Usage information
@@ -882,7 +994,7 @@ Imports management:
 
 Editor utilities:
 * validate_idranges:	Make sure your ID ranges file is formatted correctly
-* normalize_src:	Load and safe your phenio-edit file after you to make sure its serialised correctly
+* normalize_src:	Load and save your phenio-edit file after you to make sure its serialised correctly
 * explain_unsat:	If you have unsatisfiable classes, this command will create a markdown file (tmp/explain_unsat.md) which will explain all your unsatisfiable classes
 * validate-all-tsv:	Check all your tsv files for possible problems in syntax. Use ALL_TSV_FILES variable to list files
 * validate-tsv:		Check a tsv file for syntactic problems with tsvalid. Use TSV variable to pass filepath, e.g. make TSV=../my.tsv validate-tsv.
diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
index ad0e94a..2594850 100644
--- a/src/ontology/catalog-v001.xml
+++ b/src/ontology/catalog-v001.xml
@@ -61,6 +61,8 @@
 
   
   <uri name="http://purl.obolibrary.org/obo/phenio/components/bfo.owl" uri="components/bfo.owl"/>
+
+  <uri name="http://purl.obolibrary.org/obo/phenio/components/ddpheno.owl" uri="components/ddpheno.owl"/>
   
   <uri name="http://purl.obolibrary.org/obo/phenio/components/emapa.owl" uri="components/emapa.owl"/>
 
diff --git a/src/ontology/phenio-edit.owl b/src/ontology/phenio-edit.owl
index 3681815..9e3940d 100644
--- a/src/ontology/phenio-edit.owl
+++ b/src/ontology/phenio-edit.owl
@@ -12,6 +12,7 @@ Prefix(dcterms:=<http://purl.org/dc/terms/>)
 Ontology(<http://purl.obolibrary.org/obo/phenio.owl>
 
 Import(<http://purl.obolibrary.org/obo/phenio/components/bfo.owl>)
+Import(<http://purl.obolibrary.org/obo/phenio/components/ddpheno.owl>)
 Import(<http://purl.obolibrary.org/obo/phenio/components/emapa.owl>)
 #Import(<http://purl.obolibrary.org/obo/phenio/components/fao.owl>)
 Import(<http://purl.obolibrary.org/obo/phenio/components/fbbt.owl>)
diff --git a/src/ontology/phenio-odk.yaml b/src/ontology/phenio-odk.yaml
index 5257ac4..159062f 100644
--- a/src/ontology/phenio-odk.yaml
+++ b/src/ontology/phenio-odk.yaml
@@ -72,6 +72,12 @@ components:
 #      make_base: TRUE
 #      base_iris:
 #        - http://purl.obolibrary.org/obo/FAO_
+    - filename: ddpheno.owl
+      source: http://purl.obolibrary.org/obo/ddpheno.owl
+      make_base: TRUE
+      base_iris:
+        - http://purl.obolibrary.org/obo/ddpheno#
+        - http://purl.obolibrary.org/obo/DDPHENO_
     - filename: emapa.owl
       source: http://purl.obolibrary.org/obo/emapa.owl
       make_base: TRUE
diff --git a/src/ontology/run.sh b/src/ontology/run.sh
index 38545d1..fa98da3 100755
--- a/src/ontology/run.sh
+++ b/src/ontology/run.sh
@@ -14,6 +14,8 @@
 #
 # See README-editors.md for more details.
 
+set -e
+
 if [ -f run.sh.conf ]; then
     . ./run.sh.conf
 fi
@@ -29,6 +31,22 @@ elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/tok
     GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token")
 fi
 
+# SSH agent socket
+# On macOS, we cannot use $SSH_AUTH_SOCK directly,
+# we need to use a "magic" socket instead.
+case "$(uname)" in
+Darwin)
+    ODK_SSH_AUTH_SOCKET=/run/host-services/ssh-auth.sock
+    ;;
+*)
+    ODK_SSH_AUTH_SOCKET=$SSH_AUTH_SOCK
+    ;;
+esac
+ODK_SSH_BIND=
+if [ -n "$ODK_SSH_AUTH_SOCKET" ]; then
+    ODK_SSH_BIND=",$ODK_SSH_AUTH_SOCKET:/run/host-services/ssh-auth.sock"
+fi
+
 ODK_IMAGE=${ODK_IMAGE:-odkfull}
 TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }')
 if [ -n "$TAG_IN_IMAGE" ]; then
@@ -40,16 +58,28 @@ ODK_TAG=${ODK_TAG:-latest}
 ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx30G}
 ODK_DEBUG=${ODK_DEBUG:-no}
 
+ODK_USER_ID=${ODK_USER_ID:-$(id -u)}
+ODK_GROUP_ID=${ODK_GROUP_ID:-$(id -g)}
+
+# Convert OWLAPI_* environment variables to the OWLAPI as Java options
+# See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html
+# for a list of allowed options
+OWLAPI_OPTIONS_NAMESPACE=org.semanticweb.owlapi.model.parameters.ConfigurationOptions
+for owlapi_var in $(env | sed -n s/^OWLAPI_//p) ; do
+    ODK_JAVA_OPTS="$ODK_JAVA_OPTS -D$OWLAPI_OPTIONS_NAMESPACE.${owlapi_var%=*}=${owlapi_var#*=}"
+done
+
 TIMECMD=
 if [ x$ODK_DEBUG = xyes ]; then
     # If you wish to change the format string, take care of using
     # non-breaking spaces (U+00A0) instead of normal spaces, to
     # prevent the shell from tokenizing the format string.
-    echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps."
+    echo "Running obolibrary/${ODK_IMAGE}:${ODK_TAG} with '${ODK_JAVA_OPTS}' as options for ROBOT and other Java-based pipeline steps."
     TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb"
 fi
+rm -f tmp/debug.log
 
-VOLUME_BIND=$PWD/../../:/work
+VOLUME_BIND=$PWD/../../:/work$ODK_SSH_BIND
 WORK_DIR=/work/src/ontology
 
 if [ -n "$ODK_BINDS" ]; then
@@ -59,14 +89,14 @@ fi
 if [ -n "$USE_SINGULARITY" ]; then
     
     singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \
-        --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \
+        --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS,SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock,ODK_USER_ID=$ODK_USER_ID,ODK_GROUP_ID=$ODK_GROUP_ID,ODK_DEBUG=$ODK_DEBUG" \
         --bind $VOLUME_BIND \
         -W $WORK_DIR \
         docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
 else
     BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')"
     docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \
-        -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \
+        -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" -e SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock -e ODK_USER_ID=$ODK_USER_ID -e ODK_GROUP_ID=$ODK_GROUP_ID -e ODK_DEBUG=$ODK_DEBUG \
         --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@"
 fi
 
diff --git a/src/scripts/run-command.sh b/src/scripts/run-command.sh
new file mode 100755
index 0000000..45d431d
--- /dev/null
+++ b/src/scripts/run-command.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+ODK_DEBUG_FILE=${ODK_DEBUG_FILE:-debug.log}
+echo "Command: sh $@" >> $ODK_DEBUG_FILE
+/usr/bin/time -a -o $ODK_DEBUG_FILE -f "Elapsed time: %E\nPeak memory: %M kb" /bin/sh "$@"
diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh
index 7e93248..941b891 100644
--- a/src/scripts/update_repo.sh
+++ b/src/scripts/update_repo.sh
@@ -26,7 +26,8 @@ cp target/$OID/src/ontology/run.sh $SRCDIR/ontology/
 cp -r target/$OID/src/sparql/* $SRCDIR/sparql/
 mkdir -p $ROOTDIR/.github
 mkdir -p $ROOTDIR/.github/workflows
-cp -n target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml
+cp target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml
+
 
 
 cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml
@@ -35,5 +36,5 @@ cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml
 cp -n target/$OID/mkdocs.yaml $ROOTDIR/
 
 echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)"
-echo "WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml."
+
 echo "Ontology repository update successfully completed."
\ No newline at end of file
diff --git a/src/sparql/dc-properties-violation.sparql b/src/sparql/dc-properties-violation.sparql
new file mode 100644
index 0000000..e1cbfbb
--- /dev/null
+++ b/src/sparql/dc-properties-violation.sparql
@@ -0,0 +1,11 @@
+# The purpose of this violation is to make sure people update
+# from using the deprecated DC Elements 1.1 namespace (http://purl.org/dc/elements/1.1/)
+# to using the recommended DC Terms namespace (http://purl.org/dc/terms/)
+# See also discussion on https://github.com/oborel/obo-relations/pull/692
+
+SELECT ?term ?predicate WHERE {
+  ?term ?predicate ?value .
+  FILTER(STRSTARTS(STR(?predicate), "http://purl.org/dc/elements/1.1/"))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/PHENIO_")))
+}
+
diff --git a/src/sparql/illegal-date-violation.sparql b/src/sparql/illegal-date-violation.sparql
index 25ec660..9e05358 100644
--- a/src/sparql/illegal-date-violation.sparql
+++ b/src/sparql/illegal-date-violation.sparql
@@ -1,10 +1,12 @@
 PREFIX dct: <http://purl.org/dc/terms/>
 PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
 
 SELECT DISTINCT ?term ?property ?value WHERE
 {
-  VALUES ?property {dct:date dct:issued dct:created}
+  VALUES ?property {dct:date dct:issued dct:created oboInOwl:creation_date}
   ?term ?property ?value .
   FILTER (datatype(?value) != xsd:date || !regex(str(?value), '^\\d{4}-\\d\\d-\\d\\d$'))
+  FILTER (datatype(?value) != xsd:dateTime || !regex(str(?value), '^\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}Z'))
 }