diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index 8383a740c..96c3fb83f 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -1249,8 +1249,8 @@ EXTERNAL_SSSOM_PROVIDERS = fbbt cl biomappings # All the sets coming from the above ontologies. EXTERNAL_SSSOM_SETS = $(foreach provider, $(EXTERNAL_SSSOM_PROVIDERS), $(MAPPINGDIR)/$(provider).sssom.tsv) -# We only refresh external resources under IMP=true -ifeq ($(strip $(IMP)),true) +# We only refresh external resources under MIR=true +ifeq ($(strip $(MIR)),true) # FBbt mapping set. We filter it to only keep UBERON-related mappings # (CL-related mappings are already bundled with the CL set). @@ -1296,7 +1296,7 @@ endif ifeq ($(BRI),true) # Those bridges are generated separately (see below). -CUSTOM_BRIDGES = $(BRIDGEDIR)/uberon-bridge-to-mba.owl \ +EXTERN_BRIDGES = $(BRIDGEDIR)/uberon-bridge-to-mba.owl \ $(BRIDGEDIR)/uberon-bridge-to-dmba.owl # 1. Prepare the ruleset file. @@ -1312,7 +1312,7 @@ $(TMPDIR)/bridges.rules: $(SCRIPTSDIR)/sssomt.m4 $(BRIDGEDIR)/bridges.rules.m4 $(TMPDIR)/bridges: $(SRC) $(IMPORTDIR)/local-cl.owl \ $(MAPPINGDIR)/uberon.sssom.tsv $(MAPPINGDIR)/cl.sssom.tsv \ $(TMPDIR)/bridges.rules $(BRIDGEDIR)/bridges.dispatch \ - $(CUSTOM_BRIDGES) | all_robot_plugins + $(EXTERN_BRIDGES) | all_robot_plugins $(ROBOT) merge -i $(SRC) -i $(IMPORTDIR)/local-cl.owl \ sssom:inject --sssom $(MAPPINGDIR)/uberon.sssom.tsv \ --sssom $(MAPPINGDIR)/cl.sssom.tsv \ @@ -1342,8 +1342,8 @@ UBERON_BRIDGE_MBA = "https://raw.githubusercontent.com/brain-bican/mouse_brain_a UBERON_BRIDGE_DMBA = "https://raw.githubusercontent.com/brain-bican/developing_mouse_brain_atlas_ontology/main/src/ontology/new-bridges/new-uberon-bridge-to-dmba.owl" # Only refresh those bridges when we explicitly allow refreshing -# external resources (IMP=true). -ifeq ($(strip $(IMP)),true) +# external resources (MIR=true). +ifeq ($(strip $(MIR)),true) $(BRIDGEDIR)/uberon-bridge-to-mba.owl: $(SRC) $(ROBOT) annotate -I $(UBERON_BRIDGE_MBA) --ontology-iri $(ONTBASE)/$@ -o $@ @@ -1408,7 +1408,7 @@ DEPLOY_GH=true .PHONY: uberon uberon: - $(MAKE) prepare_release IMP=false PAT=false BRI=true CLEANFILES=tmp/merged-uberon-edit.obo + $(MAKE) prepare_release MIR=false IMP=false PAT=false BRI=true CLEANFILES=tmp/merged-uberon-edit.obo $(MAKE) release-diff if [ $(DEPLOY_GH) = true ]; then $(MAKE) deploy_release GHVERSION="v$(TODAY)"; fi @@ -1489,15 +1489,15 @@ clean: clean_uberon .PHONY: refresh-mappings refresh-mappings: - $(MAKE) MIR=true IMP=true $(EXTERNAL_SSSOM_SETS) + $(MAKE) MIR=true $(EXTERNAL_SSSOM_SETS) .PHONY: refresh-bridges refresh-bridges: - $(MAKE) MIR=true IMP=true BRI=true tmp/bridges + $(MAKE) MIR=true BRI=true tmp/bridges .PHONY: refresh-external-resources refresh-external-resources: - $(MAKE) MIR=true IMP=true BRI=true PAT=false IMP_LARGE=true all_imports all_local_imports tmp/bridges + $(MAKE) MIR=true IMP=true BRI=true PAT=false IMP_LARGE=true all_imports all_local_imports $(EXTERNAL_SSSOM_SETS) $(EXTERN_BRIDGES) # ----------------------------------------