Exact synonym updates (#600)

- Update: remaps IAO:0000118 (alt label) to oboInOwl:exactSynonym - Add: exact_syn_from_label.ru: adds oboInOwl:exactSynonym for all rdfs:label for all non-obsolete terms in components - Update: component goals to use new query
monarch-initiative · Aug 2, 2024 · a37945d · a37945d
1 parent 08192ca
commit a37945d
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Showing 3 changed files with 21 additions and 1 deletion.
diff --git a/src/ontology/config/property-map.sssom.tsv b/src/ontology/config/property-map.sssom.tsv
@@ -6,3 +6,4 @@ http://www.ebi.ac.uk/efo/definition	http://purl.obolibrary.org/obo/IAO_0000115
 http://www.ebi.ac.uk/efo/reason_for_obsolescence	rdfs:comment
 http://www.ebi.ac.uk/efo/alternative_term	oboInOwl:hasExactSynonym
 http://purl.obolibrary.org/obo/ECO_0000218	oboInOwl:source
+http://purl.obolibrary.org/obo/IAO_0000118	oboInOwl:hasExactSynonym
diff --git a/src/ontology/mondo-ingest.Makefile b/src/ontology/mondo-ingest.Makefile
@@ -71,6 +71,7 @@ $(COMPONENTSDIR)/omim.owl: $(TMPDIR)/omim_relevant_signature.txt | component-dow
 			--update ../sparql/fix_omimps.ru \
 			--update ../sparql/fix-labels-with-brackets.ru \
 			--update ../sparql/fix_illegal_punning_omim.ru \
+			--update ../sparql/exact_syn_from_label.ru \
 		annotate --ontology-iri $(URIBASE)/mondo/sources/omim.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/omim.owl -o $@; fi
 
 # todo: See #1 at top of file
@@ -84,6 +85,7 @@ $(COMPONENTSDIR)/ordo.owl: $(TMPDIR)/ordo_relevant_signature.txt config/properti
 			--update ../sparql/fix_complex_reification_ordo.ru \
 			--update ../sparql/fix_xref_prefixes.ru \
 			--update ../sparql/fix-labels-with-brackets.ru \
+			--update ../sparql/exact_syn_from_label.ru \
 			--update ../sparql/ordo-construct-subclass-from-part-of.ru \
 			--update ../sparql/ordo-construct-subsets.ru \
 			--update ../sparql/ordo-construct-d2g.ru \
@@ -95,7 +97,9 @@ $(COMPONENTSDIR)/ordo.owl: $(TMPDIR)/ordo_relevant_signature.txt config/properti
 $(COMPONENTSDIR)/ncit.owl: $(TMPDIR)/ncit_relevant_signature.txt | component-download-ncit.owl
 	if [ $(SKIP_HUGE) = false ] && [ $(COMP) = true ]; then $(ROBOT) remove -i $(TMPDIR)/component-download-ncit.owl.owl --select imports \
 		rename --mappings config/property-map.sssom.tsv --allow-missing-entities true --allow-duplicates true \
-		query --update ../sparql/rm_xref_by_prefix.ru \
+		query \
+			--update ../sparql/rm_xref_by_prefix.ru \
+			--update ../sparql/exact_syn_from_label.ru \
 		remove -T $(TMPDIR)/ncit_relevant_signature.txt --select complement --select "classes individuals" --trim false \
 		remove -T config/properties.txt --select complement --select properties --trim true \
 		remove --term "http://purl.obolibrary.org/obo/NCIT_C179199" --axioms "equivalent" \
@@ -112,6 +116,7 @@ $(COMPONENTSDIR)/doid.owl: $(TMPDIR)/doid_relevant_signature.txt | component-dow
 			--update ../sparql/fix-labels-with-brackets.ru \
 			--update ../sparql/rm_xref_by_prefix.ru \
 			--update ../sparql/fix_make_omim_exact.ru \
+			--update ../sparql/exact_syn_from_label.ru \
 		remove -T config/properties.txt --select complement --select properties --trim true \
 		annotate --ontology-iri $(URIBASE)/mondo/sources/doid.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/doid.owl -o $@; fi
 
@@ -136,6 +141,7 @@ $(COMPONENTSDIR)/icd10cm.owl: $(TMPDIR)/icd10cm_relevant_signature.txt | compone
 		query \
 			--update ../sparql/fix_omimps.ru \
 			--update ../sparql/fix-labels-with-brackets.ru \
+			--update ../sparql/exact_syn_from_label.ru \
 		remove -T config/properties.txt --select complement --select properties --trim true \
 		annotate --ontology-iri $(URIBASE)/mondo/sources/icd10cm.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/icd10cm.owl -o $@; fi
 
@@ -148,6 +154,7 @@ $(COMPONENTSDIR)/icd10who.owl: $(TMPDIR)/icd10who_relevant_signature.txt | compo
 		query \
 			--update ../sparql/fix_omimps.ru \
 			--update ../sparql/fix-labels-with-brackets.ru \
+			--update ../sparql/exact_syn_from_label.ru \
 		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
 
@@ -159,6 +166,7 @@ $(COMPONENTSDIR)/icd11foundation.owl: $(TMPDIR)/icd11foundation_relevant_signatu
 		remove -T $(TMPDIR)/icd11foundation_relevant_signature.txt --select individuals \
 		query \
 			--update ../sparql/fix-labels-with-brackets.ru \
+			--update ../sparql/exact_syn_from_label.ru \
 		remove -T config/properties.txt --select complement --select properties --trim true \
 		annotate --ontology-iri $(URIBASE)/mondo/sources/icd11foundation.owl --version-iri $(URIBASE)/mondo/sources/$(TODAY)/icd11foundation.owl -o $@; fi
 

diff --git a/src/sparql/exact_syn_from_label.ru b/src/sparql/exact_syn_from_label.ru
@@ -0,0 +1,11 @@
+# Create an exact synonym copy for all labels
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+INSERT {
+  ?cls oboInOwl:hasExactSynonym ?label .
+} WHERE {
+  ?cls rdfs:label ?label .
+  FILTER NOT EXISTS { ?cls owl:deprecated ?deprecated . }
+}