Added new terms in response to Mondo restructuring and added template…

… for adding tem replaced by annotation to imported obsoleted terms with another term

src/ontology/Makefile

@@ -141,7 +141,7 @@ edit_diff: efo_edit_git_diff.txt efo_edit_robot_diff.txt
 D2P_SOURCES=hpoa mondo-owl
 D2P_RAW=$(foreach V,$(D2P_SOURCES), components/d2p_$V.ttl)
 
-COMPONENTS=subclasses mondo_efo_import anatomagram_lung anatomagram_kidney anatomagram_pancreas anatomagram_liver
+COMPONENTS=subclasses import_replaced_by mondo_efo_import anatomagram_lung anatomagram_kidney anatomagram_pancreas anatomagram_liver
 COMPONENT_FILES=$(patsubst %, components/%.owl, $(COMPONENTS))
 FOREIGN_AXIOMS=hancestro uberon
 FOREIGN_AXIOM_FILES=$(patsubst %, components/efo_%.owl, $(FOREIGN_AXIOMS))
@@ -153,6 +153,9 @@ components/subclasses.owl: ../templates/subclasses.csv
 components/d2p_%.ttl: mirror/%.owl
 	$(ROBOT) query -f ttl -i $< --query $(SPARQLDIR)/d2p-$*.ru $@
 
+components/import_replaced_by.owl: ../templates/import_replaced_by.csv
+	$(ROBOT) template --template $< --prefix $(MONDOPREFIX) --prefix "snap: http://www.ifomis.org/bfo/1.1/snap#" --prefix $(EFOPREFIX) --prefix $(UBERONPREFIX) --prefix $(HPPREFIX) --ontology-iri "http://www.ebi.ac.uk/efo/components/import_replaced_by.owl" -o $@
+
 components/efo-rename.tsv: components/mondo_efo_mappings.tsv components/disease_to_phenotype_merged_signature.tsv
 	python3 ../scripts/rename_tsv_subset.py $^ $@
 

src/ontology/catalog-v001.xml

@@ -3,6 +3,7 @@
     <uri id="Imports Wizard Entry" name="http://www.ebi.ac.uk/efo/components/disease_to_phenotype.owl" uri="components/disease_to_phenotype.owl"/>
     <group id="Folder Repository, directory=, recursive=true, Auto-Update=false, version=2" prefer="public" xml:base="">
         <uri id="subclasses" name="http://www.ebi.ac.uk/efo/components/subclasses.owl" uri="components/subclasses.owl"/>
+        <uri id="import_replaced_by" name="http://www.ebi.ac.uk/efo/components/import_replaced_by.owl" uri="components/import_replaced_by.owl"/>
         <uri id="hancestro_import" name="http://www.ebi.ac.uk/efo/imports/hancestro_import.owl" uri="imports/hancestro_import.owl"/>
         <uri id="mondo_efo_import" name="http://www.ebi.ac.uk/efo/components/mondo_efo_import.owl" uri="components/mondo_efo_import.owl"/>
         <uri id="uberon_import" name="http://www.ebi.ac.uk/efo/imports/uberon_import.owl" uri="imports/uberon_import.owl"/>