Various updates to mass obsoletion pipeline (#6680)

* Various updates to mass obsoletion - Add mondo version with manipulated labels - Remove comments from mass obsoletion Pipeline - automatically add the correct axiom annotation to obsoletion reason. * Update mondo.Makefile * obsolete children of breast disorder - deficient breast volume or number - excess breast volume or number close #6684 * reclassify terms * add superclass * remove superclasses --------- Co-authored-by: Nicole Vasilevsky <[email protected]>
monarch-initiative · Sep 21, 2023 · bd58ccc · bd58ccc
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diff --git a/.gitignore b/.gitignore
@@ -106,3 +106,4 @@ src/ontology/mondo-ingest.db
 src/ontology/subsets/mondo-rare.owl
 subsets/mondo-rare.owl
 src/ontology/imports/*_terms_combined.txt
+src/ontology/config/obsolete_me.txt
diff --git a/src/ontology/mondo-edit.obo b/src/ontology/mondo-edit.obo
@@ -130209,8 +130209,8 @@ xref: Orphanet:180176 {source="OMIM:113670", source="MONDO:equivalentTo"}
 xref: UMLS:C0405471 {source="OMIM:113670", source="MONDO:notFoundInDiseaseSubset"}
 xref: UMLS:C2676048 {source="MONDO:ncbi_mim2gene_medline", source="MONDO:notFoundInDiseaseSubset"}
 xref: UMLS:CN226754 {source="MONDO:equivalentTo"}
+is_a: MONDO:0002657 {source="https://orcid.org/0000-0001-5208-3432"} ! breast disorder
 is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease
-is_a: MONDO:0015852 {source="Orphanet:180176"} ! excess breast volume or number
 property_value: confidence "8.333333333333334" xsd:double
 
 [Term]
@@ -155366,7 +155366,6 @@ xref: Orphanet:2036 {source="MONDO:equivalentTo", source="GARD:0000159", source=
 xref: SCTID:721888002 {source="MONDO:equivalentTo"}
 xref: UMLS:C1867020 {source="Orphanet:2036", source="MONDO:ncbi_mim2gene_medline", source="MONDO:notFoundInDiseaseSubset", source="Orphanet:2036/e", source="OMIM:181270"}
 is_a: MONDO:0015161 {source="Orphanet:2036"} ! multiple congenital anomalies/dysmorphic syndrome without intellectual disability
-is_a: MONDO:0015853 {source="Orphanet:2036"} ! deficient breast volume or number
 is_a: MONDO:0019287 {source="Orphanet:2036"} ! ectodermal dysplasia syndrome
 is_a: MONDO:0019294 {source="Orphanet:2036"} ! mixed dermis disorder
 relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/18249 {source="MONDO:mim2gene_medgen"} ! KCTD1
@@ -155551,10 +155550,7 @@ xref: SCTID:700211007 {source="MONDO:equivalentTo"}
 xref: UMLS:C1866994 {source="Orphanet:3138", source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="Orphanet:3138/e", source="DOID:0060614", source="OMIM:181450"}
 is_a: MONDO:0015160 {source="Orphanet:3138"} ! multiple congenital anomalies/dysmorphic syndrome-variable intellectual disability syndrome
 is_a: MONDO:0015246 {source="Orphanet:3138"} ! syndromic anorectal malformation
-is_a: MONDO:0015853 {source="Orphanet:3138"} ! deficient breast volume or number
-is_a: MONDO:0018234 ! dysostosis
 is_a: MONDO:0018454 {source="MONDO:0018455-obsoleted"} ! dysostosis of genetic origin
-is_a: MONDO:0019054 ! congenital limb malformation
 is_a: MONDO:0019713 {source="PMID:31633310"} ! non-syndromic limb reduction defect
 relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/11602 {source="MONDO:mim2gene_medgen"} ! TBX3
 property_value: confidence "46.61904761904762" xsd:double
@@ -223274,12 +223270,8 @@ xref: OMIM:603543 {source="MONDO:equivalentTo", source="Orphanet:69085", source=
 xref: Orphanet:69085 {source="OMIM:603543", source="MONDO:equivalentTo"}
 xref: SCTID:721972001 {source="MONDO:equivalentTo"}
 xref: UMLS:C1863753 {source="OMIM:603543", source="MONDO:ncbi_mim2gene_medline", source="MONDO:notFoundInDiseaseSubset", source="Orphanet:69085", source="Orphanet:69085/e"}
-is_a: MONDO:0015853 {source="Orphanet:69085"} ! deficient breast volume or number
-is_a: MONDO:0018234 ! dysostosis
-is_a: MONDO:0018454 {source="MONDO:0018455-obsoleted"} ! dysostosis of genetic origin
-is_a: MONDO:0019054 ! congenital limb malformation
+is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease
 is_a: MONDO:0020197 {source="Orphanet:69085"} ! EEC syndrome and related syndrome
-is_a: MONDO:0800090 {source="PMID:31633310"} ! ectrodactyly with and without other manifestations
 relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/15979 {source="MONDO:mim2gene_medgen"} ! TP63
 property_value: confidence "8.375" xsd:double
 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4948" xsd:anyURI
@@ -226890,7 +226882,7 @@ property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/4064/okamoto
 [Term]
 id: MONDO:0011500
 name: Becker nevus syndrome
-def: "Becker nevus syndrome is characterized by the presence of a Becker nevus in association withunderdevelopment (hypoplasia)of the breast or other skin-related, muscular, or skeletal defects, all of which usually involve the same side of the bodyas the nevus (ipsilateral). Specific signs and symptoms in addition to the nevus may include ipsilateral breast hypoplasia;skeletal abnormalities such ashypoplasia of the shoulder girdle, scoliosis, fused ribs, and ipsilateral shortness of the arm; and several other features. Thecondition is thought to be sporadic (occurring in individuals with no history of the condition in the family). Treatment varies depending upon the specific symptoms present and the extent of the condition in the affected individual." [https://rarediseases.info.nih.gov/diseases/3856/becker-nevus-syndrome]
+def: "Becker nevus syndrome is characterized by the presence of a Becker nevus in association with underdevelopment (hypoplasia) of the breast or other skin-related, muscular, or skeletal defects, all of which usually involve the same side of the bodyas the nevus (ipsilateral). Specific signs and symptoms in addition to the nevus may include ipsilateral breast hypoplasia; skeletal abnormalities such ashypoplasia of the shoulder girdle, scoliosis, fused ribs, and ipsilateral shortness of the arm; and several other features. Thecondition is thought to be sporadic (occurring in individuals with no history of the condition in the family). Treatment varies depending upon the specific symptoms present and the extent of the condition in the affected individual." [https://rarediseases.info.nih.gov/diseases/3856/becker-nevus-syndrome]
 subset: gard_rare {source="GARD:0003856"}
 subset: ordo_disease {source="Orphanet:64755"}
 synonym: "Becker nevus syndrome" EXACT [OMIM:604919]
@@ -226903,7 +226895,6 @@ xref: Orphanet:64755 {source="MONDO:equivalentTo", source="OMIM:604919"}
 xref: UMLS:C0263579 {source="Orphanet:64755"}
 xref: UMLS:C1858042 {source="Orphanet:64755", source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="OMIM:604919"}
 is_a: MONDO:0005073 {source="Orphanet:64755"} ! melanocytic nevus
-is_a: MONDO:0015853 {source="Orphanet:64755"} ! deficient breast volume or number
 is_a: MONDO:0015950 {source="Orphanet:64755"} ! inherited skin tumor
 is_a: MONDO:0019755 ! developmental defect during embryogenesis
 relationship: has_characteristic MONDO:0021136 {source="MONDO:0017414"} ! rare
@@ -266386,7 +266377,6 @@ xref: Orphanet:238744 {source="MONDO:equivalentTo", source="OMIM:613689"}
 xref: SCTID:718679004 {source="MONDO:equivalentTo"}
 xref: UMLS:C3150946 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_medline", source="OMIM:613689"}
 is_a: MONDO:0002263 {source="MONDO:Redundant", source="Orphanet:238744"} ! female reproductive system disorder
-is_a: MONDO:0015852 {source="Orphanet:238744"} ! excess breast volume or number
 is_a: MONDO:0018234 ! dysostosis
 is_a: MONDO:0018454 {source="MONDO:0018455-obsoleted"} ! dysostosis of genetic origin
 is_a: MONDO:0019054 ! congenital limb malformation
@@ -313624,29 +313614,21 @@ is_obsolete: true
 
 [Term]
 id: MONDO:0015852
-name: excess breast volume or number
-comment: Reason of obsoletion: out of scope - MONDO:excludeGroupingClass. This is part of a large mass-obsoletione effort for ORDO terms.
-subset: disease_grouping
-subset: obsoletion_candidate
+name: obsolete excess breast volume or number
 subset: ordo_group_of_disorders {source="Orphanet:180170"}
-xref: Orphanet:180170 {source="MONDO:equivalentTo"}
-is_a: MONDO:0002263 {source="MONDO:0015851-obsoleted"} ! female reproductive system disorder
-is_a: MONDO:0002657 {source="MONDO:0015851-obsoleted"} ! breast disorder
+xref: Orphanet:180170 {source="MONDO:obsoleteEquivalent"}
+property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeGrouping"}
 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5114" xsd:anyURI
-property_value: IAO:0006012 "2023-09-01" xsd:string
+is_obsolete: true
 
 [Term]
 id: MONDO:0015853
-name: deficient breast volume or number
-comment: Reason of obsoletion: out of scope - MONDO:excludeGroupingClass. This is part of a large mass-obsoletione effort for ORDO terms.
-subset: disease_grouping
-subset: obsoletion_candidate
+name: obsolete deficient breast volume or number
 subset: ordo_group_of_disorders {source="Orphanet:180173"}
-xref: Orphanet:180173 {source="MONDO:equivalentTo"}
-is_a: MONDO:0002263 {source="MONDO:0015851-obsoleted"} ! female reproductive system disorder
-is_a: MONDO:0002657 {source="MONDO:0015851-obsoleted"} ! breast disorder
+xref: Orphanet:180173 {source="MONDO:obsoleteEquivalent"}
+property_value: IAO:0000231 OMO:0001000 {source="MONDO:excludeGrouping"}
 property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5114" xsd:anyURI
-property_value: IAO:0006012 "2023-09-01" xsd:string
+is_obsolete: true
 
 [Term]
 id: MONDO:0015854
@@ -313658,7 +313640,7 @@ xref: ICD10CM:Q83.1 {source="Orphanet:180182", source="Orphanet:180182/e"}
 xref: MedDRA:10049786 {source="Orphanet:180182", source="Orphanet:180182/e"}
 xref: Orphanet:180182 {source="MONDO:equivalentTo"}
 xref: UMLS:C0266010 {source="Orphanet:180182", source="MONDO:notFoundInDiseaseSubset", source="Orphanet:180182/e"}
-is_a: MONDO:0015852 {source="Orphanet:180182"} ! excess breast volume or number
+is_a: MONDO:0002657 {source="https://orcid.org/0000-0001-5208-3432"} ! breast disorder
 
 [Term]
 id: MONDO:0015855
@@ -313670,8 +313652,8 @@ xref: ICD10CM:Q83.0 {source="Orphanet:180188/e", source="Orphanet:180188/specifi
 xref: OMIMPS:113700 {source="MONDO:equivalentTo"}
 xref: Orphanet:180188 {source="MONDO:equivalentTo"}
 xref: UMLS:C0432357 {source="MONDO:notFoundInDiseaseSubset", source="Orphanet:180188"}
-is_a: MONDO:0002263 {source="Orphanet:180188"} ! female reproductive system disorder
-is_a: MONDO:0015853 {source="Orphanet:180188"} ! deficient breast volume or number
+is_a: MONDO:0002657 {source="https://orcid.org/0000-0001-5208-3432"} ! breast disorder
+relationship: excluded_subClassOf MONDO:0002263 {source="Orphanet:180188"} ! female reproductive system disorder
 relationship: has_characteristic MONDO:0021136 {source="MONDO:0015980"} ! rare
 relationship: has_characteristic MONDO:0021152 {source="OMIMPS:113700"} ! inherited
 
@@ -313682,7 +313664,7 @@ subset: disease_grouping
 subset: ordo_group_of_disorders {source="Orphanet:180193"}
 xref: Orphanet:180193 {source="MONDO:equivalentTo"}
 xref: UMLS:CN226755 {source="MONDO:equivalentTo"}
-is_a: MONDO:0015853 {source="Orphanet:180193"} ! deficient breast volume or number
+is_a: MONDO:0002657 {source="https://orcid.org/0000-0001-5208-3432"} ! breast disorder
 
 [Term]
 id: MONDO:0015857

diff --git a/src/ontology/mondo.Makefile b/src/ontology/mondo.Makefile
@@ -483,6 +483,9 @@ mass_obsolete:
 tmp/mass_obsolete.sparql: ../sparql/reports/mondo-obsolete-simple.sparql config/obsolete_me.txt
 	LISTT="$(shell paste -sd" " config/obsolete_me.txt)"; sed "s/MONDO:0000000/$$LISTT/g" $< > $@
 
+tmp/mondo-rename-effected-classes.ru: ../sparql/reports/mondo-rename-effected-classes.ru config/obsolete_me.txt
+	LISTT="$(shell paste -sd" " config/obsolete_me.txt)"; sed "s/MONDO:0000000/$$LISTT/g" $< > $@
+
 tmp/mass_obsolete_warning.sparql: ../sparql/reports/mondo-obsolete-warning.sparql config/obsolete_me.txt
 	LISTT="$(shell paste -sd" " config/obsolete_me.txt)"; sed "s/MONDO:0000000/$$LISTT/g" $< > $@
 
@@ -501,13 +504,20 @@ mass_obsolete_warning: tmp/mass_obsolete_warning.sparql
 
 mass_obsolete2: tmp/mass_obsolete.ru tmp/mass_obsolete_me.txt
 	echo "Make sure you have updated config/obsolete_me.txt before running this script.."
-	make mass_obsolete_warning
+	$(MAKE) tmp/mondo-obsolete-labels.obo
+	$(MAKE) mass_obsolete_warning
 	$(ROBOT) query -i $(SRC) --use-graphs true --update tmp/mass_obsolete.ru \
 		remove --preserve-structure false -T tmp/mass_obsolete_me.txt --axioms logical convert -f obo --check false -o $(SRC).obo
 	mv $(SRC).obo $(SRC)
-	make NORM
+	$(MAKE) NORM
 	mv NORM $(SRC)
 
+tmp/mondo-obsolete-labels.obo: tmp/mondo-rename-effected-classes.ru
+	$(ROBOT) merge -i $(SRC) --collapse-import-closure false query --update tmp/mondo-rename-effected-classes.ru  \
+		convert -f obo --check false -o $@
+
+
+
 MAPPINGSDIR=mappings
 METADATADIR=metadata
 MAPPING_IDS=mondo
@@ -848,6 +858,7 @@ update-gard-mappings:
 	# make NORM
 	# mv NORM $(SRC)
 
+
 #######################################
 ### New Pattern merge pipeline ########
 #######################################

diff --git a/src/scripts/obsolete_me.txt b/src/scripts/obsolete_me.txt
diff --git a/src/sparql/reports/mondo-rename-effected-classes.ru b/src/sparql/reports/mondo-rename-effected-classes.ru
@@ -0,0 +1,35 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+prefix owl: <http://www.w3.org/2002/07/owl#>
+prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+prefix MONDO: <http://purl.obolibrary.org/obo/MONDO_>
+
+DELETE {
+	 ?entity rdfs:label ?label .
+}
+INSERT {
+	 ?entity rdfs:label ?new_label .
+}
+WHERE {
+  VALUES ?entity { MONDO:0000000 }  .
+    ?entity rdfs:label ?label .
+    ?entity oboInOwl:inSubset <http://purl.obolibrary.org/obo/mondo#obsoletion_candidate> .
+
+    ?xref_anno a owl:Axiom ;
+           owl:annotatedSource ?entity ;
+           owl:annotatedProperty ?property ;
+           owl:annotatedTarget ?value ;
+           oboInOwl:source ?source .
+
+  	OPTIONAL {
+  		?entity oboInOwl:inSubset ?subset .
+    	FILTER(?subset != <http://purl.obolibrary.org/obo/mondo#obsoletion_candidate> )
+  	}
+
+  	OPTIONAL {
+  		?entity <http://purl.obolibrary.org/obo/IAO_0006012> ?date .
+  	}
+
+   	FILTER NOT EXISTS { ?entity owl:deprecated true }  	
+  	BIND(CONCAT("OBSOL_BRANCH ",str(?label)) as ?new_label)
+}
diff --git a/src/sparql/update/mondo-obsolete-simple.ru b/src/sparql/update/mondo-obsolete-simple.ru
@@ -7,6 +7,7 @@ prefix MONDO: <http://purl.obolibrary.org/obo/MONDO_>
 DELETE {
   ?entity <http://purl.obolibrary.org/obo/IAO_0006012> ?date .
   ?entity oboInOwl:inSubset ?subset . #this does not delete nested subsets (ie subsets with dbxrefs)
+  ?entity rdfs:comment ?comment .
   ?entity oboInOwl:inSubset <http://purl.obolibrary.org/obo/mondo#obsoletion_candidate> .
   ?xref_anno oboInOwl:source ?source . #this deletes MONDO:equivalentTo 
   ?entity rdfs:label ?label . #this deletes the old label and adds the new label
@@ -21,6 +22,11 @@ INSERT {
   ?entity <http://purl.obolibrary.org/obo/IAO_0000231> <http://purl.obolibrary.org/obo/OMO_0001000> .
   ?entity <http://purl.obolibrary.org/obo/IAO_0000115> ?obsolete_definition .
   ?def_anno owl:annotatedTarget ?obsolete_definition.
+  [] rdf:type owl:Axiom ;
+           owl:annotatedSource ?entity ;
+           owl:annotatedProperty <http://purl.obolibrary.org/obo/IAO_0000231> ;
+           owl:annotatedTarget <http://purl.obolibrary.org/obo/OMO_0001000> ;
+           oboInOwl:source "MONDO:excludeGrouping" .
 }
 
 WHERE {
@@ -42,6 +48,10 @@ WHERE {
   	OPTIONAL {
   		?entity <http://purl.obolibrary.org/obo/IAO_0006012> ?date .
   	}
+
+    OPTIONAL {
+  		?entity rdfs:comment ?comment .
+  	}
 
     OPTIONAL {
   		?entity <http://purl.obolibrary.org/obo/IAO_0000115> ?definition .