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Added new terms in response to Mondo restructuring and added template… #2155

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Dec 14, 2023
Merged

Added new terms in response to Mondo restructuring and added template… #2155

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24,985 changes: 22,684 additions & 2,301 deletions efo-base.owl
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5 changes: 4 additions & 1 deletion src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
Expand All @@ -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 $^ $@

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1 change: 1 addition & 0 deletions src/ontology/catalog-v001.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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"/>
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