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+http://purl.obolibrary.org/obo/MONDO_0049221 https://identifiers.org/hgnc/710 "OMIM:301010" MONDO:OMIM https://omim.org/entry/301770 diff --git a/src/ontology/mondo-ingest.Makefile b/src/ontology/mondo-ingest.Makefile index 34e8c2675..f162417a8 100644 --- a/src/ontology/mondo-ingest.Makefile +++ b/src/ontology/mondo-ingest.Makefile @@ -553,12 +553,11 @@ $(REPORTDIR)/%.subclass.confirmed.robot.tsv $(REPORTDIR)/%.subclass.added.robot. ################################## ## Externally managed content #### ################################## +# General +update-externally-managed-content: external-content-nord external-content-nando external-content-ordo external-content-omim EXTERNAL_CONTENT_DIR=external -$(TMPDIR)/nord.tsv: - wget "https://rdbdev.wpengine.com/wp-content/uploads/mondo-export/rare_export.tsv" -O $@ - $(EXTERNAL_CONTENT_DIR)/%.robot.owl: $(EXTERNAL_CONTENT_DIR)/%.robot.tsv $(ROBOT) template \ --template $< \ @@ -569,19 +568,28 @@ $(EXTERNAL_CONTENT_DIR)/%.robot.owl: $(EXTERNAL_CONTENT_DIR)/%.robot.tsv -o $@ .PRECIOUS: $(EXTERNAL_CONTENT_DIR)/%.robot.owl +# NORD +.PHONY: external-content-nord +external-content-nord: $(EXTERNAL_CONTENT_DIR)/nord.robot.tsv $(EXTERNAL_CONTENT_DIR)/nord.robot.owl + +$(TMPDIR)/nord.tsv: + wget "https://rdbdev.wpengine.com/wp-content/uploads/mondo-export/rare_export.tsv" -O $@ + $(EXTERNAL_CONTENT_DIR)/nord.robot.tsv: $(TMPDIR)/nord.tsv config/external-content-robot-headers.json mkdir -p $(EXTERNAL_CONTENT_DIR) python ../scripts/add-robot-template-header.py $^ > $@ .PRECIOUS: $(EXTERNAL_CONTENT_DIR)/nord.robot.tsv -.PHONY: external-content-nord -external-content-nord: $(EXTERNAL_CONTENT_DIR)/nord.robot.tsv $(EXTERNAL_CONTENT_DIR)/nord.robot.owl +# ORDO +.PHONY: external-content-ordo +external-content-ordo: $(EXTERNAL_CONTENT_DIR)/ordo-subsets.robot.owl $(EXTERNAL_CONTENT_DIR)/ordo-subsets.robot.tsv tmp/ordo-subsets.tsv: $(MAKE) component-download-ordo.owl $(ROBOT) query -i $(TMPDIR)/component-download-ordo.owl.owl --query ../sparql/select-ordo-subsets.sparql $@ $(EXTERNAL_CONTENT_DIR)/ordo-subsets.robot.tsv: tmp/ordo-subsets.tsv tmp/mondo.sssom.tsv + mkdir -p $(EXTERNAL_CONTENT_DIR) python3 $(SCRIPTSDIR)/ordo_subsets.py \ --mondo-mappings-path tmp/mondo.sssom.tsv \ --class-subsets-tsv-path tmp/ordo-subsets.tsv \ @@ -589,8 +597,18 @@ $(EXTERNAL_CONTENT_DIR)/ordo-subsets.robot.tsv: tmp/ordo-subsets.tsv tmp/mondo.s --outpath $@ .PRECIOUS: $(EXTERNAL_CONTENT_DIR)/ordo-subsets.robot.tsv -.PHONY: external-content-ordo -external-content-ordo: $(EXTERNAL_CONTENT_DIR)/ordo-subsets.robot.owl $(EXTERNAL_CONTENT_DIR)/ordo-subsets.robot.tsv +# OMIM +$(EXTERNAL_CONTENT_DIR)/mondo_genes.robot.tsv: + mkdir -p $(EXTERNAL_CONTENT_DIR) + wget "https://github.com/monarch-initiative/omim/releases/latest/download/mondo_genes.robot.tsv" -O $@ +.PRECIOUS: $(EXTERNAL_CONTENT_DIR)/mondo_genes.robot.tsv + +.PHONY: external-content-omim +external-content-omim: $(EXTERNAL_CONTENT_DIR)/mondo_genes.robot.owl $(EXTERNAL_CONTENT_DIR)/mondo_genes.robot.tsv + +# NanDO +.PHONY: external-content-nando +external-content-nando: $(EXTERNAL_CONTENT_DIR)/nando-mappings.robot.owl $(MAPPINGSDIR)/mondo-nando.sssom.tsv: $(MAPPINGSDIR)/nando-mondo.sssom.tsv sssom invert $(MAPPINGSDIR)/nando-mondo.sssom.tsv --no-merge-inverted -o $@ @@ -601,12 +619,6 @@ $(EXTERNAL_CONTENT_DIR)/nando-mappings.robot.tsv: $(MAPPINGSDIR)/mondo-nando.sss python ../scripts/sssom_to_robot_template.py --inpath $< --outpath $@ .PRECIOUS: $(EXTERNAL_CONTENT_DIR)/nando-mappings.robot.tsv -.PHONY: external-content-nord external-content-nando -external-content-nord: $(EXTERNAL_CONTENT_DIR)/nord.robot.owl -external-content-nando: $(EXTERNAL_CONTENT_DIR)/nando-mappings.robot.owl - -update-externally-managed-content: external-content-nord external-content-nando external-content-ordo - ############################# ######### Analysis ########## #############################