ICD11 Ingest

- Update: mondo-ingest.Makefile
  - Add: $(COMPONENTSDIR)/icd11.owl

WIP

src/ontology/Makefile

@@ -54,7 +54,7 @@ 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)/doid.owl $(COMPONENTSDIR)/gard.owl $(COMPONENTSDIR)/icd10cm.owl $(COMPONENTSDIR)/icd10who.owl $(COMPONENTSDIR)/icd11foundation.owl $(COMPONENTSDIR)/ncit.owl $(COMPONENTSDIR)/omim.owl $(COMPONENTSDIR)/ordo.owl
+OTHER_SRC =                 $(COMPONENTSDIR)/doid.owl $(COMPONENTSDIR)/gard.owl $(COMPONENTSDIR)/icd10cm.owl $(COMPONENTSDIR)/icd10who.owl $(COMPONENTSDIR)/icd11foundation.owl $(COMPONENTSDIR)/ncit.owl $(COMPONENTSDIR)/omim.owl $(COMPONENTSDIR)/ordo.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 

src/ontology/mondo-ingest.Makefile

@@ -163,6 +163,22 @@ $(COMPONENTSDIR)/icd10who.owl: $(TMPDIR)/icd10who_relevant_signature.txt | compo
 		remove -T config/properties.txt --select complement --select properties --trim true \
 		annotate --ontology-iri $(URIBASE)/mondo/sources/icd10who.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/icd10who.owl -o $@; fi
 
+# TODO: do
+# TODO: remove any unnecessary queries / lines here
+#  - fix_hgnc_mappings
+#  - maybe make a comment about other ones i thought to delete
+$(COMPONENTSDIR)/icd11.owl: $(TMPDIR)/icd11_relevant_signature.txt | component-download-icd11.owl
+	if [ $(COMP) = true ] ; then $(ROBOT) remove -i $(TMPDIR)/component-download-icd11.owl.owl --select imports \
+		rename --mappings config/property-map-1.sssom.tsv --allow-missing-entities true \
+		remove -T $(TMPDIR)/icd11_relevant_signature.txt --select complement --select "classes individuals" --trim false \
+		remove -T $(TMPDIR)/icd11_relevant_signature.txt --select individuals \
+		query \
+			--update ../sparql/fix-labels-with-brackets.ru \
+			--update ../sparql/fix_hgnc_mappings.ru \
+			--update ../sparql/fix_complex_reification.ru \
+		remove -T config/properties.txt --select complement --select properties --trim true \
+		annotate --ontology-iri $(URIBASE)/mondo/sources/icd11.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/icd11.owl -o $@; fi
+
 .PHONY: component-download-gard.owl
 component-download-gard.owl: | $(TMPDIR)
 	if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I https://github.com/monarch-initiative/gard/releases/latest/download/gard.owl \