diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
index 97394937..5eb9ffb9 100644
--- a/.github/workflows/build.yaml
+++ b/.github/workflows/build.yaml
@@ -16,7 +16,7 @@ jobs:
   build:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.2.32
+    container: obolibrary/odkfull:v1.3.0
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
index 22c9d9cb..d27fc94a 100644
--- a/src/ontology/Makefile
+++ b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for bdso
 # Generated using ontology-development-kit
-# ODK Version: v1.2.32
+# ODK Version: v1.3.0
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use bdso.Makefile instead
 
@@ -28,6 +28,9 @@ RELEASEDIR=                 ../..
 REPORTDIR=                  reports
 TEMPLATEDIR=                ../templates
 TMPDIR=                     tmp
+MIRRORDIR=                  mirror
+IMPORTDIR=                  imports
+SUBSETDIR=                  subsets
 SCRIPTSDIR=                 ../scripts
 SPARQLDIR =                 ../sparql
 COMPONENTSDIR =             components
@@ -35,9 +38,9 @@ REPORT_FAIL_ON =            None
 REPORT_LABEL =              -l true
 REPORT_PROFILE_OPTS =       
 OBO_FORMAT_OPTIONS =        
-SPARQL_VALIDATION_CHECKS =   equivalent-classes owldef-self-reference
-SPARQL_EXPORTS =             basic-report class-count-by-prefix edges xrefs obsoletes synonyms
-ODK_VERSION_MAKEFILE =      v1.2.32
+SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri 
+SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
+ODK_VERSION_MAKEFILE =      v1.3.0
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
@@ -46,8 +49,7 @@ ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --anno
 OTHER_SRC =                 $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/all_templates.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 PATTERNDIR=                 ../patterns
-DOSDP_SCHEMA=                http:// # change to PURL when ready.
-PATTERN_TESTER=              simple_pattern_tester.py
+PATTERN_TESTER=              dosdp validate -i
 DOSDPT=                      dosdp-tools
 PATTERN_RELEASE_FILES=       $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.owl
 
@@ -64,10 +66,10 @@ RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-simple-non-classified $(ONT)-full
 .PHONY: .FORCE
 
 .PHONY: all
-all: odkversion all_imports patterns all_main all_subsets sparql_test all_reports all_assets
+all: odkversion test all_assets
 
 .PHONY: test
-test: odkversion sparql_test all_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt
+test: odkversion dosdp_validation sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt
 	$(ROBOT) reason --input $(SRC) --reasoner ELK  --equivalent-classes-allowed asserted-only --exclude-tautologies structural --output test.owl && rm test.owl && echo "Success"
 
 .PHONY: odkversion
@@ -75,28 +77,29 @@ 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
 
-$(TMPDIR) $(REPORTDIR) :
+$(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR):
 	mkdir -p $@
 
-## -- main targets --
-##
-## By default this is the cross-product of {ont, ont-base} x FORMATS
+# ----------------------------------------
+# Release assets
+# ----------------------------------------
 
 MAIN_PRODUCTS = $(sort $(foreach r,$(RELEASE_ARTEFACTS), $(r)) $(ONT))
-MAIN_GZIPPED = 
-MAIN_FILES = $(foreach n,$(MAIN_PRODUCTS), $(foreach f,$(FORMATS), $(n).$(f))) $(MAIN_GZIPPED)
+MAIN_GZIPPED  = 
+MAIN_FILES    = $(foreach n,$(MAIN_PRODUCTS), $(foreach f,$(FORMATS), $(n).$(f))) $(MAIN_GZIPPED)
+SRCMERGED     = $(TMPDIR)/merged-$(SRC)
 
 .PHONY: all_main
 all_main: $(MAIN_FILES)
 
-## -- import targets --
-##
-## By default this is the cross-product of IMPORT_MODULES x FORMATS
+# ----------------------------------------
+# Import assets
+# ----------------------------------------
 
 
 IMPORTS =  pr go ro uberon pato cl ensmusg ncbitaxon
 
-IMPORT_ROOTS = $(patsubst %, imports/%_import, $(IMPORTS))
+IMPORT_ROOTS =  $(IMPORTDIR)/merged_import
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
 IMPORT_FILES = $(IMPORT_OWL_FILES)
 
@@ -104,20 +107,23 @@ IMPORT_FILES = $(IMPORT_OWL_FILES)
 .PHONY: all_imports
 all_imports: $(IMPORT_FILES)
 
-## -- subset targets --
-##
-## By default this is the cross-product of SUBSETS x FORMATS
-## Note we also include TSV as a format
+# ----------------------------------------
+# Subset assets
+# ----------------------------------------
 
 
 SUBSETS = 
 
-SUBSET_ROOTS = $(patsubst %, subsets/%, $(SUBSETS))
+SUBSET_ROOTS = $(patsubst %, $(SUBSETDIR)/%, $(SUBSETS))
 SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f)))
 
 .PHONY: all_subsets
 all_subsets: $(SUBSET_FILES)
 
+# ----------------------------------------
+# QC Reports & Utilities
+# ----------------------------------------
+
 OBO_REPORT =  $(SRC)-obo-report
 REPORTS = $(OBO_REPORT)
 REPORT_FILES = $(patsubst %, $(REPORTDIR)/%.tsv, $(REPORTS))
@@ -126,20 +132,53 @@ REPORT_FILES = $(patsubst %, $(REPORTDIR)/%.tsv, $(REPORTS))
 robot_reports: $(REPORT_FILES)
 
 .PHONY: all_reports
-all_reports: all_reports_onestep $(REPORT_FILES)
+all_reports: custom_reports robot_reports
+
+# ----------------------------------------
+# ROBOT OWL Profile checking
+# ----------------------------------------
 
-$(REPORTDIR)/validate_profile_owl2dl_%.txt: % | $(REPORTDIR)
-	$(ROBOT) validate-profile --profile DL -i $< -o $@
+# The conversion to functional syntax is necessary to avoid undeclared entity violations.
+$(REPORTDIR)/validate_profile_owl2dl_%.txt: % | $(REPORTDIR) $(TMPDIR)
+	$(ROBOT) merge -i $< convert -f ofn -o $(TMPDIR)/validate.ofn
+	$(ROBOT) validate-profile --profile DL -i $(TMPDIR)/validate.ofn -o $@ || { cat $@ && exit 1; }
 .PRECIOUS: $(REPORTDIR)/validate_profile_owl2dl_%.txt
 
-.PHONY: validate_profile_%
 validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt
+	echo "$* profile validation completed."
+
+# ----------------------------------------
+# Sparql queries: Q/C
+# ----------------------------------------
 
-## -- all files/assets --
+# these live in the ../sparql directory, and have suffix -violation.sparql
+# adding the name here will make the violation check live.
+
+SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql)
+
+sparql_test: $(SRC) catalog-v001.xml | $(REPORTDIR)
+ifneq ($(SPARQL_VALIDATION_QUERIES),)
+	$(ROBOT) verify  --catalog catalog-v001.xml -i $< --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
+endif
+
+# ----------------------------------------
+# ROBOT report
+# ----------------------------------------
+
+$(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR)
+	$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
+
+$(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR)
+	$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
+
+# ----------------------------------------
+# Release assets
+# ----------------------------------------
 
 ASSETS = \
   $(IMPORT_FILES) \
   $(MAIN_FILES) \
+  $(PATTERN_RELEASE_FILES) \
   $(REPORT_FILES) \
   $(SUBSET_FILES)
 
@@ -150,13 +189,11 @@ RELEASE_ASSETS = \
 .PHONY: all_assets
 all_assets: $(ASSETS)
 
-
 .PHONY: show_assets
 show_assets:
 	echo $(ASSETS)
 	du -sh $(ASSETS)
 
-
 # ----------------------------------------
 # Release Management
 # ----------------------------------------
@@ -166,33 +203,28 @@ CLEANFILES=$(MAIN_FILES) $(SRCMERGED)
 # It will ensure that all assets/files are fresh, and will copy to release folder
 
 .PHONY: prepare_release
-prepare_release: $(ASSETS) $(PATTERN_RELEASE_FILES)
+prepare_release: all
 	rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\
-  mkdir -p $(RELEASEDIR)/patterns &&\
-  cp $(PATTERN_RELEASE_FILES) $(RELEASEDIR)/patterns &&\
-  rm -f $(CLEANFILES) &&\
-  echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab"
+	mkdir -p $(RELEASEDIR)/patterns && cp -rf $(PATTERN_RELEASE_FILES) $(RELEASEDIR)/patterns &&\
+	rm -f $(CLEANFILES) &&\
+	echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release on your git hosting site such as GitHub or GitLab"
 
 .PHONY: prepare_initial_release
-prepare_initial_release: prepare_release
+prepare_initial_release: all_assets
+	rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\
+	mkdir -p $(RELEASEDIR)/patterns && cp -rf $(PATTERN_RELEASE_FILES) $(RELEASEDIR)/patterns &&\
+	rm -f $(patsubst %, ./%, $(CLEANFILES)) &&\
 	cd $(RELEASEDIR) && git add $(RELEASE_ASSETS)
 
-# ----------------------------------------
-# Import modules
-# ----------------------------------------
-# Most ontologies are modularly constructed using portions of other ontologies
-# These live in the imports/ folder
-
 # ------------------------
 # Imports: Seeding system 
 # ------------------------
 
 # seed.txt contains all referenced entities
 IMPORTSEED=$(TMPDIR)/seed.txt
-SRCMERGED=$(TMPDIR)/merged-$(SRC)
 PRESEED=$(TMPDIR)/pre_seed.txt
 
-$(SRCMERGED): $(SRC)
+$(SRCMERGED): $(SRC) $(OTHER_SRC)
 	$(ROBOT) remove --input $< --select imports --trim false \
 		merge  $(patsubst %, -i %, $(OTHER_SRC)) -o $@
 
@@ -209,51 +241,53 @@ $(SIMPLESEED): $(SRCMERGED) $(ONTOLOGYTERMS)
 	echo "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty" >> $@
 
 
-ALLSEED = $(PRESEED)  $(PATTERNDIR)/all_pattern_terms.txt \
+ALLSEED = $(PRESEED)  $(TMPDIR)/all_pattern_terms.txt \
 
 
-$(IMPORTSEED):  prepare_patterns  $(ALLSEED) 
+$(IMPORTSEED): $(ALLSEED) | $(TMPDIR)
 	if [ $(IMP) = true ]; then cat $(ALLSEED) | sort | uniq > $@; fi
 
-
 ANNOTATION_PROPERTIES=rdfs:label IAO:0000115 
 
-# -- Generate Import Modules --
-#
+# ----------------------------------------
+# Import modules
+# ----------------------------------------
+# Most ontologies are modularly constructed using portions of other ontologies
+# These live in the imports/ folder
 # This pattern uses ROBOT to generate an import module
-# Generate terms.txt for each import.  (Assume OBO-style Possibly hacky step?)
+
 # Should be able to drop this if robot can just take a big messy list of terms as input.
-imports/%_terms_combined.txt: $(IMPORTSEED) imports/%_terms.txt
+$(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt
 	if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq >  $@; fi
 
 
-ALL_TERMS_COMBINED = $(patsubst %, imports/%_terms_combined.txt, $(IMPORTS))
-imports/merged_terms_combined.txt: $(ALL_TERMS_COMBINED)
+ALL_TERMS_COMBINED = $(patsubst %, $(IMPORTDIR)/%_terms_combined.txt, $(IMPORTS))
+$(IMPORTDIR)/merged_terms_combined.txt: $(ALL_TERMS_COMBINED)
 	if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq >  $@; fi
 
 
-imports/merged_import.owl: mirror/merged.owl imports/merged_terms_combined.txt
+$(IMPORTDIR)/merged_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/merged_terms_combined.txt
 	if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \
 		remove  --select "<http://www.informatics.jax.org/marker/MGI:*>" remove  --select "<http://purl.obolibrary.org/obo/OBA_*>" remove  --select "<http://purl.obolibrary.org/obo/ENVO_*>" remove  --select "<http://purl.obolibrary.org/obo/OBI_*>" remove  --select "<http://purl.obolibrary.org/obo/GOCHE_*>" remove  --select "<http://purl.obolibrary.org/obo/CARO_*>" remove  --select "<http://purl.obolibrary.org/obo/NCBITaxon_Union_*>" remove  --select "<http://www.genenames.org/cgi-bin/gene_symbol_report*>"  \
-		extract -T imports/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
+		extract -T $(IMPORTDIR)/merged_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
 		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
 
 
 
 
-imports/%_import.owl: mirror/merged.owl imports/%_terms_combined.txt
+$(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/%_terms_combined.txt
 	if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \
-		extract -T imports/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
+		extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals exclude --method BOT \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
 		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
 
-.PRECIOUS: imports/%_import.owl
+.PRECIOUS: $(IMPORTDIR)/%_import.owl
 
 ## Module for ontology: pr
 
-imports/pr_import.owl: mirror/merged.owl imports/pr_terms_combined.txt
-	if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T imports/pr_terms_combined.txt --force true --individuals exclude --method BOT \
+$(IMPORTDIR)/pr_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/pr_terms_combined.txt
+	if [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) extract -i $< -T $(IMPORTDIR)/pr_terms_combined.txt --force true --individuals exclude --method BOT \
 		query --update ../sparql/inject-subset-declaration.ru --update ../sparql/postprocess-module.ru \
 		annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@; fi
 
@@ -265,18 +299,17 @@ refresh-imports:
 no-mirror-refresh-imports:
 	make IMP=true MIR=false PAT=false IMP_LARGE=true all_imports -B
 
-
 .PHONY: refresh-imports-excluding-large
 refresh-imports-excluding-large:
 	make IMP=true MIR=true PAT=false IMP_LARGE=false all_imports -B
 
 .PHONY: refresh-%
 refresh-%:
-	make IMP=true IMP_LARGE=true MIR=true PAT=false imports/$*_import.owl -B
+	make IMP=true IMP_LARGE=true MIR=true PAT=false $(IMPORTDIR)/$*_import.owl -B
 
 .PHONY: no-mirror-refresh-%
 no-mirror-refresh-%:
-	make IMP=true IMP_LARGE=true MIR=false PAT=false imports/$*_import.owl -B
+	make IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B
 
 
 # ----------------------------------------
@@ -284,7 +317,9 @@ no-mirror-refresh-%:
 # ----------------------------------------
 # Some ontologies contain external and internal components. A component is included in the ontology in its entirety.
 
-$(COMPONENTSDIR)/%:
+COMP=true # Global parameter to bypass component generation
+
+$(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
 	touch $@
 .PRECIOUS: $(COMPONENTSDIR)/%
 
@@ -292,97 +327,83 @@ $(COMPONENTSDIR)/%:
 
 
 
-
-
 # ----------------------------------------
 # Mirroring upstream ontologies
 # ----------------------------------------
-#
 
 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
-PAT=true # Global parameter to bypass pattern generation
 
-## ONTOLOGY: pr
-## Copy of pr is re-downloaded whenever source changes
-mirror/pr.trigger: $(SRC)
 
-mirror/pr.owl: mirror/pr.trigger
+
+## ONTOLOGY: pr
+.PHONY: mirror-pr
+.PRECIOUS: $(MIRRORDIR)/pr.owl
+mirror-pr: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(IMP) = true ] && [ $(IMP_LARGE) = true ]; then $(ROBOT) convert -I https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/PR --axioms external --preserve-structure false --trim false -o $@.tmp.owl && mv $@.tmp.owl $@; fi
-.PRECIOUS: mirror/pr.owl
+		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/PR --axioms external --preserve-structure false --trim false -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: go
-## Copy of go is re-downloaded whenever source changes
-mirror/go.trigger: $(SRC)
-
-mirror/go.owl: mirror/go.trigger
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/go/go-base.owl --create-dirs -o mirror/go.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/go.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi
-.PRECIOUS: mirror/go.owl
+.PHONY: mirror-go
+.PRECIOUS: $(MIRRORDIR)/go.owl
+mirror-go:
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/go/go-base.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/go.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: ro
-## Copy of ro is re-downloaded whenever source changes
-mirror/ro.trigger: $(SRC)
-
-mirror/ro.owl: mirror/ro.trigger
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/ro/ro-base.owl --create-dirs -o mirror/ro.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi
-.PRECIOUS: mirror/ro.owl
+.PHONY: mirror-ro
+.PRECIOUS: $(MIRRORDIR)/ro.owl
+mirror-ro:
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/ro/ro-base.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: uberon
-## Copy of uberon is re-downloaded whenever source changes
-mirror/uberon.trigger: $(SRC)
-
-mirror/uberon.owl: mirror/uberon.trigger
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/uberon/uberon-base.owl --create-dirs -o mirror/uberon.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/uberon.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi
-.PRECIOUS: mirror/uberon.owl
+.PHONY: mirror-uberon
+.PRECIOUS: $(MIRRORDIR)/uberon.owl
+mirror-uberon:
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/uberon/uberon-base.owl --create-dirs -o $(MIRRORDIR)/uberon.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/uberon.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: pato
-## Copy of pato is re-downloaded whenever source changes
-mirror/pato.trigger: $(SRC)
-
-mirror/pato.owl: mirror/pato.trigger
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/pato/pato-base.owl --create-dirs -o mirror/pato.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/pato.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi
-.PRECIOUS: mirror/pato.owl
+.PHONY: mirror-pato
+.PRECIOUS: $(MIRRORDIR)/pato.owl
+mirror-pato:
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/pato/pato-base.owl --create-dirs -o $(MIRRORDIR)/pato.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/pato.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: cl
-## Copy of cl is re-downloaded whenever source changes
-mirror/cl.trigger: $(SRC)
-
-mirror/cl.owl: mirror/cl.trigger
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/cl/cl-base.owl --create-dirs -o mirror/cl.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/cl.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi
-.PRECIOUS: mirror/cl.owl
+.PHONY: mirror-cl
+.PRECIOUS: $(MIRRORDIR)/cl.owl
+mirror-cl:
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/cl/cl-base.owl --create-dirs -o $(MIRRORDIR)/cl.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/cl.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: ensmusg
-## Copy of ensmusg is re-downloaded whenever source changes
-mirror/ensmusg.trigger: $(SRC)
-
-mirror/ensmusg.owl: mirror/ensmusg.trigger
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/ensmusg.owl --create-dirs -o mirror/ensmusg.owl --retry 4 --max-time 200 && $(ROBOT) convert -i mirror/ensmusg.owl -o $@.tmp.owl && \
-		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/ENSMUSG --axioms external --preserve-structure false --trim false -o $@.tmp.owl && mv $@.tmp.owl $@; fi
-.PRECIOUS: mirror/ensmusg.owl
+.PHONY: mirror-ensmusg
+.PRECIOUS: $(MIRRORDIR)/ensmusg.owl
+mirror-ensmusg: | $(TMPDIR)
+	if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/ensmusg.owl --create-dirs -o $(MIRRORDIR)/ensmusg.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/ensmusg.owl -o $@.tmp.owl && \
+		$(ROBOT) remove -i $@.tmp.owl --base-iri $(URIBASE)/ENSMUSG --axioms external --preserve-structure false --trim false -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi
 
 
 ## ONTOLOGY: ncbitaxon
-## Copy of ncbitaxon is re-downloaded whenever source changes
-mirror/ncbitaxon.trigger: $(SRC)
-
-mirror/ncbitaxon.owl: mirror/ncbitaxon.trigger
-	if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl -o $@.tmp.owl && mv $@.tmp.owl $@; fi
-.PRECIOUS: mirror/ncbitaxon.owl
+.PHONY: mirror-ncbitaxon
+.PRECIOUS: $(MIRRORDIR)/ncbitaxon.owl
+mirror-ncbitaxon: | $(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
 
-ALL_MIRRORS = $(patsubst %, mirror/%.owl, $(IMPORTS))
+ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS))
 MERGE_MIRRORS = true
 
-mirror/merged.owl: $(ALL_MIRRORS)
+$(MIRRORDIR)/merged.owl: $(ALL_MIRRORS)
 	if [ $(IMP) = true ] && [ $(MERGE_MIRRORS) = true ]; then $(ROBOT) merge $(patsubst %, -i %, $^) -o $@; fi
-.PRECIOUS: mirror/merged.owl
+.PRECIOUS: $(MIRRORDIR)/merged.owl
+
+
+$(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR)
+	if [ $(IMP) = true ] && [ $(MIR) = true ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." && cp $(TMPDIR)/mirror-$*.owl $@; fi; fi
 
 
 
@@ -390,132 +411,127 @@ mirror/merged.owl: $(ALL_MIRRORS)
 # ----------------------------------------
 # Subsets
 # ----------------------------------------
-subsets/%.tsv: subsets/%.owl
+$(SUBSETDIR)/%.tsv: $(SUBSETDIR)/%.owl
 	$(ROBOT) query -f tsv -i $< -s ../sparql/labels.sparql $@
-.PRECIOUS: subsets/%.tsv
+.PRECIOUS: $(SUBSETDIR)/%.tsv
 
-subsets/%.owl: $(ONT).owl
+$(SUBSETDIR)/%.owl: $(ONT).owl | $(SUBSETDIR)
 	$(OWLTOOLS) $< --extract-ontology-subset --fill-gaps --subset $* -o $@.tmp.owl && mv $@.tmp.owl $@ &&\
 	$(ROBOT) annotate --input $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@.tmp.owl && mv $@.tmp.owl $@
-.PRECIOUS: subsets/%.owl
+.PRECIOUS: $(SUBSETDIR)/%.owl
 
 
-subsets/%.obo: subsets/%.owl
+$(SUBSETDIR)/%.obo: $(SUBSETDIR)/%.owl
 	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
 
-subsets/%.json: subsets/%.owl
+$(SUBSETDIR)/%.json: $(SUBSETDIR)/%.owl
 	$(ROBOT) convert --input $< --check false -f json -o $@.tmp.json &&\
 	jq -S 'walk(if type == "array" then sort else . end)' $@.tmp.json > $@ && rm $@.tmp.json
 
 
-# ----------------------------------------
-# Release
-# ----------------------------------------
-# copy from staging area (this directory) to top-level
-.PHONY: release
-release: $(ONT).owl $(ONT).obo
-	cp $^ $(RELEASEDIR) && cp imports/* $(RELEASEDIR)/imports
-
-# ----------------------------------------
-# Sparql queries: Q/C
-# ----------------------------------------
-
-# these live in the ../sparql directory, and have suffix -violation.sparql
-# adding the name here will make the violation check live.
-# NOTE: these will soon be phased out and replaced by robot-report
-
-#  run all violation checks
-SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql)
-sparql_test: $(SRC) catalog-v001.xml | $(REPORTDIR)
-ifneq ($(SPARQL_VALIDATION_QUERIES),)
-	$(ROBOT) verify  --catalog catalog-v001.xml -i $< --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR)
-endif
-
-# ----------------------------------------
-# ROBOT report
-# ----------------------------------------
-
-$(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR)
-	$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
-
-$(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR)
-	$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
-
-# ----------------------------------------
-# Sparql queries: Exports
-# ----------------------------------------
+# ---------------------------------------------
+# Sparql queries: Table exports / Query Reports
+# ---------------------------------------------
 
 SPARQL_EXPORTS_ARGS = $(foreach V,$(SPARQL_EXPORTS),-s $(SPARQLDIR)/$(V).sparql $(REPORTDIR)/$(V).tsv)
 # This combines all into one single command
 
-.PHONY: all_reports_onestep
-all_reports_onestep: $(SRC) | $(REPORTDIR)
+.PHONY: custom_reports
+custom_reports: $(SRC) | $(REPORTDIR)
 ifneq ($(SPARQL_EXPORTS_ARGS),)
 	$(ROBOT) query -f tsv -i $< $(SPARQL_EXPORTS_ARGS)
 endif
 # ----------------------------------------
-# Patterns (experimental)
+# DOSDP Templates/Patterns
 # ----------------------------------------
 
-# Test patterns for schema compliance:
+PAT=true # Global parameter to bypass pattern generation
+ALL_PATTERN_FILES=$(wildcard $(PATTERNDIR)/dosdp-patterns/*.yaml)
+ALL_PATTERN_NAMES=$(strip $(patsubst %.yaml,%, $(notdir $(wildcard $(PATTERNDIR)/dosdp-patterns/*.yaml))))
 
-.PHONY: patterns
-patterns: all_imports $(PATTERNDIR)/pattern.owl $(PATTERNDIR)/definitions.owl
+PATTERN_CLEAN_FILES=../patterns/all_pattern_terms.txt \
+	$(DOSDP_OWL_FILES_DEFAULT) $(DOSDP_TERM_FILES_DEFAULT) \
+	
 
+# Note to future generations: prepending ./ is a safety measure to ensure that 
+# the environment does not malicously set `PATTERN_CLEAN_FILES` to `\`.
 .PHONY: pattern_clean
 pattern_clean:
-	echo "Not implemented"
+	rm -f $(PATTERN_CLEAN_FILES)
+
+.PHONY: patterns
+patterns dosdp:
+	echo "Validating all DOSDP templates"
+	make dosdp_validation
+	echo "Building $(PATTERNDIR)/definitions.owl"
+	make $(PATTERNDIR)/pattern.owl $(PATTERNDIR)/definitions.owl
+
+# DOSDP Template Validation
+
+$(TMPDIR)/pattern_schema_checks: $(ALL_PATTERN_FILES) | $(TMPDIR)
+	$(PATTERN_TESTER) $(PATTERNDIR)/dosdp-patterns/ && touch $@
 
 .PHONY: pattern_schema_checks
-pattern_schema_checks: update_patterns
-	$(PATTERN_TESTER) $(PATTERNDIR)/dosdp-patterns/
+pattern_schema_checks dosdp_validation: $(TMPDIR)/pattern_schema_checks
 
-#This command is a workaround for the absence of -N and -i in wget of alpine (the one ODK depend on now). It downloads all patterns specified in external.txt
 .PHONY: update_patterns
-update_patterns: .FORCE
-	if [ $(PAT) = true ]; then rm -f $(PATTERNDIR)/dosdp-patterns/*.yaml.1 || true; fi
-	if [ $(PAT) = true ] && [ -s $(PATTERNDIR)/dosdp-patterns/external.txt ]; then wget -i $(PATTERNDIR)/dosdp-patterns/external.txt --backups=1 -P $(PATTERNDIR)/dosdp-patterns; fi
-	if [ $(PAT) = true ]; then rm -f $(PATTERNDIR)/dosdp-patterns/*.yaml.1 || true; fi
+update_patterns: download_patterns
+	cp -r $(TMPDIR)/dosdp/*.yaml $(PATTERNDIR)/dosdp-patterns
 
+# This command is a workaround for the absence of -N and -i in wget of alpine (the one ODK depend on now).
+# It downloads all patterns specified in external.txt
+.PHONY: download_patterns
+download_patterns:
+	if [ $(PAT) = true ]; then rm -f $(TMPDIR)/dosdp/*.yaml.1 || true; fi
+	if [ $(PAT) = true ] && [ -s $(PATTERNDIR)/dosdp-patterns/external.txt ]; then wget -i $(PATTERNDIR)/dosdp-patterns/external.txt --backups=1 -P $(TMPDIR)/dosdp; fi
+	if [ $(PAT) = true ]; then rm -f $(TMPDIR)/dosdp/*.yaml.1 || true; fi
 
-$(PATTERNDIR)/pattern.owl: pattern_schema_checks update_patterns
-	if [ $(PAT) = true ]; then $(DOSDPT) prototype --obo-prefixes true --template=$(PATTERNDIR)/dosdp-patterns --outfile=$@; fi
+$(PATTERNDIR)/dospd-patterns/%.yml: download_patterns
+	if [ $(PAT) = true ] ; then if cmp -s $(TMPDIR)/dosdp-$*.yml $@ ; then echo "DOSDP templates identical."; else echo "DOSDP templates different, updating." && cp $(TMPDIR)/dosdp-$*.yml $@; fi; fi
 
-individual_patterns_default := $(patsubst %.tsv, $(PATTERNDIR)/data/default/%.ofn, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv)))
-pattern_term_lists_default := $(patsubst %.tsv, $(PATTERNDIR)/data/default/%.txt, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv)))
 
+# DOSDP Template: Pipelines
+# Each pipeline gets its own directory structure
 
+# DOSDP default pipeline
 
+DOSDP_TSV_FILES_DEFAULT = $(wildcard $(PATTERNDIR)/data/default/*.tsv)
+DOSDP_OWL_FILES_DEFAULT = $(patsubst %.tsv, $(PATTERNDIR)/data/default/%.ofn, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv)))
+DOSDP_TERM_FILES_DEFAULT = $(patsubst %.tsv, $(PATTERNDIR)/data/default/%.txt, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv)))
+DOSDP_PATTERN_NAMES_DEFAULT = $(strip $(patsubst %.tsv,%, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv))))
 
+$(DOSDP_OWL_FILES_DEFAULT): $(SRC) $(DOSDP_TSV_FILES_DEFAULT) $(ALL_PATTERN_FILES)
+	if [ $(PAT) = true ] && [ "${DOSDP_PATTERN_NAMES_DEFAULT}" ]; then $(DOSDPT) generate --catalog=catalog-v001.xml --infile=$(PATTERNDIR)/data/default/ --template=$(PATTERNDIR)/dosdp-patterns --batch-patterns="$(DOSDP_PATTERN_NAMES_DEFAULT)" --ontology=$< --obo-prefixes=true --outfile=$(PATTERNDIR)/data/default; fi
 
-# Generating the individual pattern modules and merging them into definitions.owl
-$(PATTERNDIR)/definitions.owl: prepare_patterns update_patterns dosdp_patterns_default  
-	if [ $(PAT) = true ] && [ "${individual_patterns_names_default}" ]   && [ $(PAT) = true ]; then $(ROBOT) merge $(addprefix -i , $(individual_patterns_default))   annotate --ontology-iri $(ONTBASE)/patterns/definitions.owl  --version-iri $(ONTBASE)/releases/$(TODAY)/patterns/definitions.owl --annotation owl:versionInfo $(VERSION) -o definitions.ofn && mv definitions.ofn $@; fi
 
-individual_patterns_names_default := $(strip $(patsubst %.tsv,%, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv))))
-dosdp_patterns_default: $(SRC) all_imports .FORCE
-	if [ $(PAT) = true ] && [ "${individual_patterns_names_default}" ]; then $(DOSDPT) generate --catalog=catalog-v001.xml --infile=$(PATTERNDIR)/data/default/ --template=$(PATTERNDIR)/dosdp-patterns --batch-patterns="$(individual_patterns_names_default)" --ontology=$< --obo-prefixes=true --outfile=$(PATTERNDIR)/data/default; fi
 
 
 
+# Generate template file seeds
+
+## Generate template file seeds
+$(PATTERNDIR)/data/default/%.txt: $(PATTERNDIR)/dosdp-patterns/%.yaml $(PATTERNDIR)/data/default/%.tsv
+	if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@; fi
+
 
 
 # Generating the seed file from all the TSVs. If Pattern generation is deactivated, we still extract a seed from definitions.owl
-$(PATTERNDIR)/all_pattern_terms.txt: $(pattern_term_lists_default)   $(PATTERNDIR)/pattern_owl_seed.txt
-	if [ $(PAT) = true ]; then cat $^ | sort | uniq > $@; else $(ROBOT) query --use-graphs true -f csv -i ../patterns/definitions.owl --query ../sparql/terms.sparql $@; fi
+$(TMPDIR)/all_pattern_terms.txt: $(DOSDP_TERM_FILES_DEFAULT)   $(TMPDIR)/pattern_owl_seed.txt
+	if [ $(PAT) = true ]; then cat $^ | sort | uniq > $@; else $(ROBOT) query --use-graphs true -f csv -i $(PATTERNDIR)/definitions.owl --query ../sparql/terms.sparql $@; fi
 
-$(PATTERNDIR)/pattern_owl_seed.txt: $(PATTERNDIR)/pattern.owl
+$(TMPDIR)/pattern_owl_seed.txt: $(PATTERNDIR)/pattern.owl
 	if [ $(PAT) = true ]; then $(ROBOT) query --use-graphs true -f csv -i $< --query ../sparql/terms.sparql $@; fi
 
-$(PATTERNDIR)/data/default/%.txt: $(PATTERNDIR)/dosdp-patterns/%.yaml $(PATTERNDIR)/data/default/%.tsv .FORCE
-	if [ $(PAT) = true ]; then $(DOSDPT) terms --infile=$(word 2, $^) --template=$< --obo-prefixes=true --outfile=$@; fi
-
-.PHONY: prepare_patterns
-prepare_patterns:
-	if [ $(PAT) = true ]; then touch $(PATTERNDIR)/data $(pattern_term_lists_default)  ; fi
-	if [ $(PAT) = true ]; then touch $(PATTERNDIR)/data $(individual_patterns_default)  ; fi
+# Pattern pipeline main targets: the generated OWL files
 
+# Create pattern.owl, an ontology of all DOSDP patterns
+$(PATTERNDIR)/pattern.owl: $(ALL_PATTERN_FILES)
+	if [ $(PAT) = true ]; then $(DOSDPT) prototype --obo-prefixes true --template=$(PATTERNDIR)/dosdp-patterns --outfile=$@; fi
 
+# Generating the individual pattern modules and merging them into definitions.owl
+$(PATTERNDIR)/definitions.owl: $(DOSDP_OWL_FILES_DEFAULT)  
+	if [ $(PAT) = true ] && [ "${DOSDP_PATTERN_NAMES_DEFAULT}" ]   && [ $(PAT) = true ]; then $(ROBOT) merge $(addprefix -i , $^) \
+		annotate --ontology-iri $(ONTBASE)/patterns/definitions.owl  --version-iri $(ONTBASE)/releases/$(TODAY)/patterns/definitions.owl --annotation owl:versionInfo $(VERSION) -o definitions.ofn && mv definitions.ofn $@; fi
 
 
 
@@ -591,7 +607,7 @@ $(ONT)-base.owl: $(SRC) $(OTHER_SRC)
 		--output $@.tmp.owl && mv $@.tmp.owl $@
 
 # Full: The full artefacts with imports merged, reasoned
-$(ONT)-full.owl: $(SRC) $(OTHER_SRC)
+$(ONT)-full.owl: $(SRC) $(OTHER_SRC) $(IMPORT_FILES)
 	$(ROBOT) merge --input $< \
 		reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
 		relax \
@@ -602,7 +618,7 @@ $(ONT)-full.owl: $(SRC) $(OTHER_SRC)
 # drop every axiom: filter --term-file keep_terms.txt --trim true
 #	remove --select imports --trim false \
 
-$(ONT)-simple.owl: $(SRC) $(OTHER_SRC) $(SIMPLESEED)
+$(ONT)-simple.owl: $(SRC) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES)
 	$(ROBOT) merge --input $< $(patsubst %, -i %, $(OTHER_SRC)) \
 		reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \
 		relax \
@@ -616,7 +632,7 @@ $(ONT)-simple.owl: $(SRC) $(OTHER_SRC) $(SIMPLESEED)
 # Should this be the non-classified ontology with the drop foreign axiom filter?
 # Consider adding remove --term "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
 
-$(ONT)-simple-non-classified.owl: $(SRC) $(OTHER_SRC) $(ONTOLOGYTERMS)
+$(ONT)-simple-non-classified.owl: $(SRC) $(OTHER_SRC) $(ONTOLOGYTERMS) $(IMPORT_FILES)
 	$(ROBOT) remove --input $< --select imports --trim true \
 		merge  $(patsubst %, -i %, $(OTHER_SRC))  \
 		remove --axioms equivalent \
@@ -632,12 +648,30 @@ explain_unsat: $(SRC)
 
 
 
+# ----------------------------------------
+# General Validation
+# ----------------------------------------
+TSV=
+ALL_TSV_FILES=$(DOSDP_TSV_FILES_DEFAULT)
+
+validate-tsv: $(TSV) | $(TMPDIR)
+	for FILE in $< ; do \
+		tsvalid $$FILE > $(TMPDIR)/validate.txt; \
+		if [ -s $(TMPDIR)/validate.txt ]; then cat $(TMPDIR)/validate.txt && exit 1; fi ; \
+	done
+
+validate-all-tsv: $(ALL_TSV_FILES)
+	make validate-tsv TSV="$^"
+
+# ----------------------------------------
+# Editors Utilities
+# ----------------------------------------
+
 
 
 .PHONY: normalize_src
 normalize_src: $(SRC)
-	$(ROBOT) convert -i $< -f ofn -o tmp/normalise && mv tmp/normalise $<
-
+	$(ROBOT) convert -i $< -f ofn -o $(TMPDIR)/normalise && mv $(TMPDIR)/normalise $<
 
 .PHONY: validate_idranges
 validate_idranges:
@@ -649,4 +683,81 @@ update_repo:
 	
 
 
+# Note to future generations: prepending ./ is a safety measure to ensure that 
+# the environment does not malicously set `CLEANFILES` to `\`.
+.PHONY: clean
+clean:
+	make pattern_clean
+	[ -n "$(MIRRORDIR)" ] && [ $(MIRRORDIR) != "." ] && [ $(MIRRORDIR) != "/" ] && [ $(MIRRORDIR) != ".." ] && [ -d ./$(MIRRORDIR) ] && rm -rf ./$(MIRRORDIR)/*
+	[ -n "$(TMPDIR)" ] && [ $(TMPDIR) != "." ] && [ $(TMPDIR) != "/" ] && [ $(TMPDIR) != ".." ] && [ -d ./$(TMPDIR) ] && rm -rf ./$(TMPDIR)/*
+	rm -f $(CLEANFILES)
+
+.PHONY: help
+help:
+	@echo "$$data"
+
+define data
+Usage: [IMAGE=(odklite|odkfull)] [ODK_DEBUG=yes] sh run.sh make [(IMP|MIR|IMP_LARGE|PAT)=(false|true)] command
+
+----------------------------------------
+	Command reference
+----------------------------------------
+
+Core commands:
+* prepare_release:	Run the entire release pipeline. Use make IMP=false prepare_release to avoid rerunning the imports
+* update_repo:		Update the ODK repository setup using the config file bdso-odk.yaml
+* test:			Running all validation tests
+* odkversion:		Show the current version of the ODK Makefile and ROBOT.
+* clean:		Delete all temporary files
+* help:			Print ODK Usage information
+
+
+Imports management:
+* refresh-imports:			Refresh all imports and mirrors.
+* no-mirror-refresh-imports:		Refresh all imports without downloading mirrors.
+* refresh-imports-excluding-large:	Refresh all imports and mirrors, but skipping the ones labelled as 'is_large'.
+* refresh-%:				Refresh a single import, i.e. refresh-go will refresh 'imports/go_import.owl'.
+* no-mirror-refresh-%:			Refresh a single import without updating the mirror, i.e. refresh-go will refresh 'imports/go_import.owl'.
+* mirror-%:				Refresh a single mirror.
+
+DOSDP templates
+* dosdp:			Run the DOSDP patterns pipeline: Run tests, then build OWL files from the tables.
+* patterns:			Alias of the 'dosdp' command
+* pattern_clean:		Delete all temporary pattern files
+* dosdp_validation:		Run all validation checks on DOSDP template files and tables
+* pattern_schema_checks:	Alias of the 'dosdp_validation' command
+* update_patterns:		Pull updated patterns listed in dosdp-patterns/external.txt
+* dosdp-matches-%:		Run the DOSDP matches/query pipeline as configured in your bdso-odk.yaml file.
+
+Editor utilities:
+* validate_idranges:	Make sure your ID ranges file is formatted correctly
+* normalize_src:	Load and safe your bdso-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.
+
+Additional build commands (advanced users)
+* all:			Run the entire pipeline (like prepare_release), but without copying the release files to the release directory.
+* all_subsets:		Build all subsets
+* custom_reports:	Generate all custom sparql reports you have configured in your bdso-odk.yaml file.
+* all_assets:		Build all assets
+* show_assets:		Print a list of all assets that would be build by the release pipeline
+
+Additional QC commands (advanced users)
+* robot_reports:	Run all configured ROBOT reports
+* validate_profile_%:	Run an OWL2 DL profile validation check, for example validate_profile_bdso-edit.owl.
+
+Examples: 
+* sh run.sh make IMP=false prepare_release
+* sh run.sh make update_repo
+* sh run.sh make test
+
+Tricks:
+* Add -B to the end of your command to force re-running it even if nothing has changed
+* Use the IMAGE parameter to the run.sh script to use a different image like odklite
+* Use ODK_DEBUG=yes sh run.sh make ... to print information about timing and debugging
+
+endef
+export data
+
 include bdso.Makefile
\ No newline at end of file
diff --git a/src/ontology/bdso.Makefile b/src/ontology/bdso.Makefile
index 3f0ca0b9..6222dac4 100644
--- a/src/ontology/bdso.Makefile
+++ b/src/ontology/bdso.Makefile
@@ -30,7 +30,7 @@ PCL_LEGACY_FILE = components/pcl-legacy.owl
 #TEMPLATE_CLASS_FILES = $(patsubst %, ../templates/_%class.tsv, $(JOBS))
 
 # overriding to add prefixes
-$(PATTERNDIR)/pattern.owl: pattern_schema_checks update_patterns
+$(PATTERNDIR)/pattern.owl: 
 	if [ $(PAT) = true ]; then $(DOSDPT) prototype --prefixes=template_prefixes.yaml --obo-prefixes true --template=$(PATTERNDIR)/dosdp-patterns --outfile=$@; fi
 
 individual_patterns_names_default := $(strip $(patsubst %.tsv,%, $(notdir $(wildcard $(PATTERNDIR)/data/default/*.tsv))))
@@ -221,8 +221,8 @@ $(ONT)-pcl-comp.json: $(RELEASEDIR)/$(ONT)-pcl-comp.owl
 		convert --check false -f json -o $@.tmp.json &&\
 	jq -S 'walk(if type == "array" then sort else . end)' $@.tmp.json > $(RELEASEDIR)/$@ && rm $@.tmp.json
 
-
-# skip schema checks for now, because odk using the wrong validator
-.PHONY: pattern_schema_checks
-pattern_schema_checks: update_patterns
-	if [ $(PAT) = "skip" ]; then $(PATTERN_TESTER) $(PATTERNDIR)/dosdp-patterns/  ; fi
\ No newline at end of file
+# New ODK should remove the need for this 
+## skip schema checks for now, because odk using the wrong validator
+##.PHONY: pattern_schema_checks
+##pattern_schema_checks: update_patterns
+##	if [ $(PAT) = "skip" ]; then $(PATTERN_TESTER) $(PATTERNDIR)/dosdp-patterns/  ; fi
\ No newline at end of file
diff --git a/src/sparql/bdso_terms.sparql b/src/sparql/bdso_terms.sparql
index 6ecc01db..4a4b18e6 100644
--- a/src/sparql/bdso_terms.sparql
+++ b/src/sparql/bdso_terms.sparql
@@ -3,5 +3,5 @@ WHERE {
   { ?s1 ?p1 ?term . }
   UNION
   { ?term ?p2 ?o2 . }
-  FILTER(isIRI(?term) && (regex(str(?term), UCASE("bdso_"))))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BDSO_")))
 }
diff --git a/src/sparql/iri-range-violation.sparql b/src/sparql/iri-range-violation.sparql
new file mode 100644
index 00000000..796ffa64
--- /dev/null
+++ b/src/sparql/iri-range-violation.sparql
@@ -0,0 +1,19 @@
+PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
+PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX dcterms: <http://purl.org/dc/terms/>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+
+SELECT ?term ?property ?value
+WHERE {
+  VALUES ?property {
+    never_in_taxon:
+    present_in_taxon:
+    foaf:depicted_by
+    oboInOwl:inSubset
+    dcterms:contributor  }
+  ?term ?property ?value .
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BDSO_")))
+  FILTER (!isIRI(?value))
+}
+
diff --git a/src/sparql/label-with-iri-violation.sparql b/src/sparql/label-with-iri-violation.sparql
new file mode 100644
index 00000000..d4828076
--- /dev/null
+++ b/src/sparql/label-with-iri-violation.sparql
@@ -0,0 +1,9 @@
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT ?term ?value
+WHERE {
+  ?term rdfs:label ?value .
+  FILTER (REGEX(?value, "http[s]?[:]"))
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BDSO_")))
+}
+
diff --git a/src/sparql/owldef-self-reference-violation.sparql b/src/sparql/owldef-self-reference-violation.sparql
index 63857fea..f2b28b1a 100644
--- a/src/sparql/owldef-self-reference-violation.sparql
+++ b/src/sparql/owldef-self-reference-violation.sparql
@@ -1,11 +1,12 @@
-prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-prefix oio: <http://www.geneontology.org/formats/oboInOwl#>
-prefix owl: <http://www.w3.org/2002/07/owl#>
-prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oio: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
-SELECT ?c
-WHERE {
-  { ?c owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?c ] ] }
+SELECT ?term WHERE {
+  { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?term ] ] }
     UNION
-  { ?c owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?c ] ] ] }
+  { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?term ] ] ] }
+  FILTER(isIRI(?term) && (STRSTARTS(str(?term), "http://purl.obolibrary.org/obo/BDSO_")))
 }
+