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Merge pull request #166 from monarch-initiative/240508-relation
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Update has foundation stock relation for cats
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@sabrinatoro
sabrinatoro authored May 9, 2024
2 parents 085dbed + 34c1860 commit dbf681c
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Showing 9 changed files with 1,334 additions and 431 deletions.
1,109 changes: 982 additions & 127 deletions src/ontology/components/catbreeds.owl
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522 changes: 261 additions & 261 deletions src/ontology/components/catbreeds.tsv
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2 changes: 1 addition & 1 deletion src/ontology/components/relation.owl
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Expand Up @@ -64,7 +64,7 @@
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<rdfs:domain rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7742"/>
<obo:IAO_0000115>A relation between two distinct material entities (breeds or species), a descendant entity and an ancestor entity, in which the descendant entity is the result of mating, manipulation, or geographical or cultural isolation of the ancestor entity, therefore inheriting some of the ancestor’s genetic material.</obo:IAO_0000115>
<obo:IAO_0000116>has_foundation_stock&quot; can be use to relate a breed to one or more other breeds, or to a &quot;species&quot; (ie an NCBITaxon term) as in the cases of &quot;hybrid breeds&quot;. &quot;Hybrid breeds&quot; are created by crossing animals of different species.</obo:IAO_0000116>
<obo:IAO_0000116>has_foundation_stock&quot; can be used to relate a breed to one or more other breeds, or to a &quot;species&quot; (ie an NCBITaxon term) as in the cases of &quot;hybrid breeds&quot;. &quot;Hybrid breeds&quot; are created by crossing animals of different species.</obo:IAO_0000116>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-4142-7153"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-5002-8648"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2024-04-11T14:49:29Z</terms:created>
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2 changes: 1 addition & 1 deletion src/ontology/components/relation.tsv
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@@ -1,3 +1,3 @@
relation id (required) type label (required) definition (required) parent relation creator ORCID (required) Date created (required) relation characteristics domain range inverse property example of use synonyms curator/usage notes
ID TYPE AL rdfs:label@en A IAO:0000115 SP % AI dc:contributor SPLIT=| AT dc:created^^xsd:dateTime CHARACTERISTIC SPLIT=| DOMAIN RANGE IP % A rdfs:comment A oboInOwl:hasExactSynonym SPLIT=| A IAO:0000116
VBO:0300019 owl:ObjectProperty has_foundation_stock A relation between two distinct material entities (breeds or species), a descendant entity and an ancestor entity, in which the descendant entity is the result of mating, manipulation, or geographical or cultural isolation of the ancestor entity, therefore inheriting some of the ancestor’s genetic material. https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5002-8648 2024-04-11T14:49:29Z Transitive NCBITaxon:7742 A "foundation stock" refers to animals that are the progenitors, or foundation, of a breed or of a given bloodline within such. Many modern breeds can be traced to specific, named foundation animals, but a group of animals may be referred to collectively as foundation bloodstock when one distinct population (including both landrace breeds or a group of animals linked to a deliberate and specific selective breeding program) provides part of the underlying genetic base for a new distinct population. (https://en.wikipedia.org/wiki/Foundation_stock.) Example of usage: 'Cymric (cat)' (VBO:0100080) has_foundation_stock 'Manx (cat)' (VBO:0100156). "has_foundation_stock" can be use to relate a breed to one or more other breeds, or to a "species" (ie an NCBITaxon term) as in the cases of "hybrid breeds". "Hybrid breeds" are created by crossing animals of different species.
VBO:0300019 owl:ObjectProperty has_foundation_stock A relation between two distinct material entities (breeds or species), a descendant entity and an ancestor entity, in which the descendant entity is the result of mating, manipulation, or geographical or cultural isolation of the ancestor entity, therefore inheriting some of the ancestor’s genetic material. https://orcid.org/0000-0002-4142-7153|https://orcid.org/0000-0002-5002-8648 2024-04-11T14:49:29Z Transitive NCBITaxon:7742 A "foundation stock" refers to animals that are the progenitors, or foundation, of a breed or of a given bloodline within such. Many modern breeds can be traced to specific, named foundation animals, but a group of animals may be referred to collectively as foundation bloodstock when one distinct population (including both landrace breeds or a group of animals linked to a deliberate and specific selective breeding program) provides part of the underlying genetic base for a new distinct population. (https://en.wikipedia.org/wiki/Foundation_stock.) Example of usage: 'Cymric (cat)' (VBO:0100080) has_foundation_stock 'Manx (cat)' (VBO:0100156). "has_foundation_stock" can be used to relate a breed to one or more other breeds, or to a "species" (ie an NCBITaxon term) as in the cases of "hybrid breeds". "Hybrid breeds" are created by crossing animals of different species.
4 changes: 2 additions & 2 deletions src/ontology/imports/cob_import.owl
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Expand Up @@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/vbo/imports/cob_import.owl>
<http://purl.obolibrary.org/obo/vbo/releases/2024-04-30/imports/cob_import.owl>
<http://purl.obolibrary.org/obo/vbo/releases/2024-05-08/imports/cob_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/cob/releases/2023-11-16/cob.owl>)
Annotation(owl:versionInfo "2024-04-30")
Annotation(owl:versionInfo "2024-05-08")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000015>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000016>))
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58 changes: 53 additions & 5 deletions src/ontology/imports/ncbitaxon_import.owl
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Expand Up @@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/vbo/imports/ncbitaxon_import.owl>
<http://purl.obolibrary.org/obo/vbo/releases/2024-04-30/imports/ncbitaxon_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ncbitaxon/releases/2024-03-26/subsets/taxslim.owl>)
Annotation(owl:versionInfo "2024-04-30")
<http://purl.obolibrary.org/obo/vbo/releases/2024-05-08/imports/ncbitaxon_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/ncbitaxon/releases/2024-05-08/subsets/taxslim.owl>)
Annotation(owl:versionInfo "2024-05-08")

Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_1>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_10040>))
Expand All @@ -27,6 +27,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_1549675>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_1963758>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_2068716>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_2068722>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_2576912>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_2607030>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_2607033>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_2759>))
Expand Down Expand Up @@ -67,6 +68,8 @@ Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_46478>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_466544>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_466552>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_6072>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_61376>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_61377>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_7711>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_7742>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_7776>))
Expand Down Expand Up @@ -125,6 +128,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9612>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9615>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9681>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9682>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9683>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9685>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9787>))
Declaration(Class(<http://purl.obolibrary.org/obo/NCBITaxon_9788>))
Expand Down Expand Up @@ -461,6 +465,15 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://pu
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_2068722> "Anserinae")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_2068722> <http://purl.obolibrary.org/obo/NCBITaxon_8830>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_2576912> (Felis chaus x Felis catus)

AnnotationAssertion(<http://purl.obolibrary.org/obo/ncbitaxon#has_rank> <http://purl.obolibrary.org/obo/NCBITaxon_2576912> <http://purl.obolibrary.org/obo/NCBITaxon_species>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_2576912> "GC_ID:1")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/NCBITaxon_2576912> "ncbi_taxonomy")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/NCBITaxon_2576912> "NCBITaxon:2576912")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_2576912> "Felis chaus x Felis catus")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_2576912> <http://purl.obolibrary.org/obo/NCBITaxon_9682>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_2607030> (Caprimulgimorphae)

AnnotationAssertion(<http://purl.obolibrary.org/obo/ncbitaxon#has_rank> <http://purl.obolibrary.org/obo/NCBITaxon_2607030> <http://purl.obolibrary.org/obo/NCBITaxon_clade>)
Expand Down Expand Up @@ -880,6 +893,30 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://pu
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_6072> "Eumetazoa")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_6072> <http://purl.obolibrary.org/obo/NCBITaxon_33208>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_61376> (Felis chaus)

AnnotationAssertion(<http://purl.obolibrary.org/obo/ncbitaxon#has_rank> <http://purl.obolibrary.org/obo/NCBITaxon_61376> <http://purl.obolibrary.org/obo/NCBITaxon_species>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_61376> "GC_ID:1")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/NCBITaxon_61376> "jungle cat")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/NCBITaxon_61376> "ncbi_taxonomy")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/NCBITaxon_61376> "NCBITaxon:61376")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_61376> "Felis chaus")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_61376> <http://purl.obolibrary.org/obo/NCBITaxon_9682>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_61377> (Felis silvestris lybica)

AnnotationAssertion(<http://purl.obolibrary.org/obo/ncbitaxon#has_rank> <http://purl.obolibrary.org/obo/NCBITaxon_61377> <http://purl.obolibrary.org/obo/NCBITaxon_subspecies>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_61377> "GC_ID:1")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_61377> "PMID:17600185")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/NCBITaxon_61377> "Near Eastern wildcat")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/NCBITaxon_61377> "ncbi_taxonomy")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/ncbitaxon#synonym>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/NCBITaxon_61377> "Felis libyca")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/ncbitaxon#synonym>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/NCBITaxon_61377> "Felis lybica")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/ncbitaxon#synonym>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/NCBITaxon_61377> "Felis silvestris libyca")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/NCBITaxon_61377> "NCBITaxon:61377")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_61377> "Felis silvestris lybica")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_61377> <http://purl.obolibrary.org/obo/NCBITaxon_9683>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_7711> (Chordata)

AnnotationAssertion(<http://purl.obolibrary.org/obo/ncbitaxon#has_rank> <http://purl.obolibrary.org/obo/NCBITaxon_7711> <http://purl.obolibrary.org/obo/NCBITaxon_phylum>)
Expand Down Expand Up @@ -1418,10 +1455,10 @@ SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_9103> <http://purl.obolibra

AnnotationAssertion(<http://purl.obolibrary.org/obo/ncbitaxon#has_rank> <http://purl.obolibrary.org/obo/NCBITaxon_91561> <http://purl.obolibrary.org/obo/NCBITaxon_order>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_91561> "GC_ID:1")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/NCBITaxon_91561> "whales, hippos, ruminants, pigs, camels etc.")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/NCBITaxon_91561> "even-toed ungulates & whales")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/NCBITaxon_91561> "ncbi_taxonomy")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/ncbitaxon#synonym>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/NCBITaxon_91561> "Cetartiodactyla")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/ncbitaxon#blast_name>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/NCBITaxon_91561> "even-toed ungulates")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/ncbitaxon#blast_name>) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/NCBITaxon_91561> "even-toed ungulates & whales")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/NCBITaxon_91561> "NCBITaxon:91561")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_91561> "Artiodactyla")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_91561> <http://purl.obolibrary.org/obo/NCBITaxon_314145>)
Expand Down Expand Up @@ -1505,6 +1542,17 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://pu
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_9682> "Felis")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_9682> <http://purl.obolibrary.org/obo/NCBITaxon_338152>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_9683> (Felis silvestris)

AnnotationAssertion(<http://purl.obolibrary.org/obo/ncbitaxon#has_rank> <http://purl.obolibrary.org/obo/NCBITaxon_9683> <http://purl.obolibrary.org/obo/NCBITaxon_species>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_9683> "GC_ID:1")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/NCBITaxon_9683> "PMID:17600185")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/NCBITaxon_9683> "wild cat")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasOBONamespace> <http://purl.obolibrary.org/obo/NCBITaxon_9683> "ncbi_taxonomy")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#id> <http://purl.obolibrary.org/obo/NCBITaxon_9683> "NCBITaxon:9683")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/NCBITaxon_9683> "Felis silvestris")
SubClassOf(<http://purl.obolibrary.org/obo/NCBITaxon_9683> <http://purl.obolibrary.org/obo/NCBITaxon_9682>)

# Class: <http://purl.obolibrary.org/obo/NCBITaxon_9685> (Felis catus)

AnnotationAssertion(<http://purl.obolibrary.org/obo/ncbitaxon#has_rank> <http://purl.obolibrary.org/obo/NCBITaxon_9685> <http://purl.obolibrary.org/obo/NCBITaxon_species>)
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4 changes: 2 additions & 2 deletions src/ontology/imports/omo_import.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/vbo/imports/omo_import.owl>
<http://purl.obolibrary.org/obo/vbo/releases/2024-04-30/imports/omo_import.owl>
<http://purl.obolibrary.org/obo/vbo/releases/2024-05-08/imports/omo_import.owl>
Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/omo/releases/2023-11-02/omo.owl>)
Annotation(owl:versionInfo "2024-04-30")
Annotation(owl:versionInfo "2024-05-08")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000031>))
Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000027>))
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