@prefix vcfr:  <https://w3id.org/vcf-rdfizer/vocab#> .
@prefix vcfc:  <https://w3id.org/vcf-core/vocab#> .
@prefix owl:   <http://www.w3.org/2002/07/owl#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix dct:   <http://purl.org/dc/terms/> .

#################################################################
# Legacy document for the retired VCF-RDFizer Vocabulary namespace
#
# Served AT https://w3id.org/vcf-rdfizer/vocab so that IRIs minted
# under version 1.1.0 keep dereferencing to the document in which
# they are defined.
#################################################################

vcfr: a owl:Ontology ;
  rdfs:label "VCF-RDFizer Vocabulary (retired namespace)"@en ;
  dct:description "Deprecation record for the retired VCF-RDFizer Vocabulary namespace. Every term defined up to version 1.1.0 is retained here as a deprecated term linked to its successor in the VCF Core Vocabulary. No new terms are added to this document."@en ;
  dct:license <https://creativecommons.org/licenses/by/4.0/> ;
  dct:creator "Elias Crum" ;
  owl:versionInfo "1.1.0-retired" ;
  dct:modified "2026-09-06"^^xsd:date ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc: ;
  rdfs:seeAlso <https://w3id.org/vcf-core/vocab> .

#################################################################
# Term-by-term successor links (95 terms)
#################################################################

vcfr:alt a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:alt ;
  owl:equivalentProperty vcfc:alt .

vcfr:AltDefinition a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:AltDefinition ;
  owl:equivalentClass vcfc:AltDefinition .

vcfr:ALTHeaderLine a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:ALTHeaderLine ;
  owl:equivalentClass vcfc:ALTHeaderLine .

vcfr:altId a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:altId ;
  owl:equivalentProperty vcfc:altId .

vcfr:appliesToSampleSet a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:appliesToSampleSet ;
  owl:equivalentProperty vcfc:appliesToSampleSet .

vcfr:asSequenceAlteration a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:asSequenceAlteration ;
  owl:equivalentProperty vcfc:asSequenceAlteration .

# Was owl:Class in 1.1.0; vcfc:CharacterType became a named individual of
# vcfc:VCFValueType in 2.0.0, so the bridge is owl:sameAs, not
# owl:equivalentClass, which would no longer be OWL 2 DL.
vcfr:CharacterType a owl:NamedIndividual ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:CharacterType ;
  owl:sameAs vcfc:CharacterType .

vcfr:chrom a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:chrom ;
  owl:equivalentProperty vcfc:chrom .

vcfr:chromosome a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:chromosome ;
  owl:equivalentProperty vcfc:chromosome .

vcfr:CohortCallMatrix a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:CohortCallMatrix ;
  owl:equivalentClass vcfc:CohortCallMatrix .

vcfr:CondensedRepresentation a owl:NamedIndividual ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:CondensedRepresentation ;
  owl:sameAs vcfc:CondensedRepresentation .

vcfr:contigAssembly a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:contigAssembly ;
  owl:equivalentProperty vcfc:contigAssembly .

vcfr:contigCount a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:contigCount ;
  owl:equivalentProperty vcfc:contigCount .

vcfr:ContigHeaderLine a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:ContigHeaderLine ;
  owl:equivalentClass vcfc:ContigHeaderLine .

vcfr:contigId a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:contigId ;
  owl:equivalentProperty vcfc:contigId .

vcfr:contigLength a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:contigLength ;
  owl:equivalentProperty vcfc:contigLength .

vcfr:contigMd5 a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:contigMd5 ;
  owl:equivalentProperty vcfc:contigMd5 .

vcfr:declaredBy a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:declaredBy ;
  owl:equivalentProperty vcfc:declaredBy .

vcfr:DenseRepresentation a owl:NamedIndividual ;
  owl:deprecated true ;
  rdfs:comment "Renamed in VCF Core Vocabulary 2.0.0. The profile the documentation has always called 'expanded' is now also named ExpandedRepresentation."@en ;
  dct:isReplacedBy vcfc:ExpandedRepresentation ;
  owl:sameAs vcfc:ExpandedRepresentation .

vcfr:encodedValues a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:encodedValues ;
  owl:equivalentProperty vcfc:encodedValues .

vcfr:FieldDefinition a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:FieldDefinition ;
  owl:equivalentClass vcfc:FieldDefinition .

vcfr:fieldDescription a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:fieldDescription ;
  owl:equivalentProperty vcfc:fieldDescription .

vcfr:fieldId a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:fieldId ;
  owl:equivalentProperty vcfc:fieldId .

vcfr:fieldNumber a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:fieldNumber ;
  owl:equivalentProperty vcfc:fieldNumber .

vcfr:fieldType a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:fieldType ;
  owl:equivalentProperty vcfc:fieldType .

vcfr:fieldValue a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:fieldValue ;
  owl:equivalentProperty vcfc:fieldValue .

vcfr:fieldValueBoolean a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:fieldValueBoolean ;
  owl:equivalentProperty vcfc:fieldValueBoolean .

vcfr:fieldValueDecimal a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:fieldValueDecimal ;
  owl:equivalentProperty vcfc:fieldValueDecimal .

vcfr:fieldValueInteger a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:fieldValueInteger ;
  owl:equivalentProperty vcfc:fieldValueInteger .

vcfr:fileDate a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:fileDate ;
  owl:equivalentProperty vcfc:fileDate .

vcfr:FileDateHeaderLine a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:FileDateHeaderLine ;
  owl:equivalentClass vcfc:FileDateHeaderLine .

vcfr:fileFormat a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:fileFormat ;
  owl:equivalentProperty vcfc:fileFormat .

vcfr:FileFormatHeaderLine a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:FileFormatHeaderLine ;
  owl:equivalentClass vcfc:FileFormatHeaderLine .

vcfr:filter a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:filter ;
  owl:equivalentProperty vcfc:filter .

vcfr:FilterDefinition a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:FilterDefinition ;
  owl:equivalentClass vcfc:FilterDefinition .

vcfr:FILTERHeaderLine a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:FILTERHeaderLine ;
  owl:equivalentClass vcfc:FILTERHeaderLine .

vcfr:filterId a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:filterId ;
  owl:equivalentProperty vcfc:filterId .

# Was owl:Class in 1.1.0; vcfc:FlagType became a named individual of
# vcfc:VCFValueType in 2.0.0, so the bridge is owl:sameAs, not
# owl:equivalentClass, which would no longer be OWL 2 DL.
vcfr:FlagType a owl:NamedIndividual ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:FlagType ;
  owl:sameAs vcfc:FlagType .

# Was owl:Class in 1.1.0; vcfc:FloatType became a named individual of
# vcfc:VCFValueType in 2.0.0, so the bridge is owl:sameAs, not
# owl:equivalentClass, which would no longer be OWL 2 DL.
vcfr:FloatType a owl:NamedIndividual ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:FloatType ;
  owl:sameAs vcfc:FloatType .

vcfr:FormatFieldDefinition a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:FormatFieldDefinition ;
  owl:equivalentClass vcfc:FormatFieldDefinition .

vcfr:FormatFieldValue a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:FormatFieldValue ;
  owl:equivalentClass vcfc:FormatFieldValue .

vcfr:FORMATHeaderLine a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:FORMATHeaderLine ;
  owl:equivalentClass vcfc:FORMATHeaderLine .

vcfr:formatRaw a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:formatRaw ;
  owl:equivalentProperty vcfc:formatRaw .

vcfr:FormatValueVector a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:FormatValueVector ;
  owl:equivalentClass vcfc:FormatValueVector .

vcfr:forSample a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:forSample ;
  owl:equivalentProperty vcfc:forSample .

vcfr:hasCall a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:hasCall ;
  owl:equivalentProperty vcfc:hasCall .

vcfr:hasCallMatrix a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:hasCallMatrix ;
  owl:equivalentProperty vcfc:hasCallMatrix .

vcfr:hasFormatValue a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:hasFormatValue ;
  owl:equivalentProperty vcfc:hasFormatValue .

vcfr:hasFormatValueVector a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:hasFormatValueVector ;
  owl:equivalentProperty vcfc:hasFormatValueVector .

vcfr:hasHeader a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:hasHeader ;
  owl:equivalentProperty vcfc:hasHeader .

vcfr:hasHeaderLine a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:hasHeaderLine ;
  owl:equivalentProperty vcfc:hasHeaderLine .

vcfr:hasInfoValue a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:hasInfoValue ;
  owl:equivalentProperty vcfc:hasInfoValue .

vcfr:hasRecord a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:hasRecord ;
  owl:equivalentProperty vcfc:hasRecord .

vcfr:hasSample a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:hasSample ;
  owl:equivalentProperty vcfc:hasSample .

vcfr:hasSampleCall a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:hasSampleCall ;
  owl:equivalentProperty vcfc:hasSampleCall .

vcfr:hasSampleSet a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:hasSampleSet ;
  owl:equivalentProperty vcfc:hasSampleSet .

vcfr:headerKey a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:headerKey ;
  owl:equivalentProperty vcfc:headerKey .

vcfr:HeaderLine a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:HeaderLine ;
  owl:equivalentClass vcfc:HeaderLine .

vcfr:headerValue a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:headerValue ;
  owl:equivalentProperty vcfc:headerValue .

vcfr:InfoFieldDefinition a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:InfoFieldDefinition ;
  owl:equivalentClass vcfc:InfoFieldDefinition .

vcfr:InfoFieldValue a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:InfoFieldValue ;
  owl:equivalentClass vcfc:InfoFieldValue .

vcfr:INFOHeaderLine a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:INFOHeaderLine ;
  owl:equivalentClass vcfc:INFOHeaderLine .

vcfr:infoRaw a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:infoRaw ;
  owl:equivalentProperty vcfc:infoRaw .

# Was owl:Class in 1.1.0; vcfc:IntegerType became a named individual of
# vcfc:VCFValueType in 2.0.0, so the bridge is owl:sameAs, not
# owl:equivalentClass, which would no longer be OWL 2 DL.
vcfr:IntegerType a owl:NamedIndividual ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:IntegerType ;
  owl:sameAs vcfc:IntegerType .

vcfr:iriTemplate a owl:AnnotationProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:iriTemplate ;
  owl:equivalentProperty vcfc:iriTemplate .

vcfr:missingValuePolicy a owl:AnnotationProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:missingValuePolicy ;
  owl:equivalentProperty vcfc:missingValuePolicy .

vcfr:Null a rdfs:Datatype ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:Null ;
  owl:equivalentClass vcfc:Null .

vcfr:pos a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:pos ;
  owl:equivalentProperty vcfc:pos .

vcfr:qual a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:qual ;
  owl:equivalentProperty vcfc:qual .

vcfr:recommendedSequenceAlterationClass a owl:AnnotationProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:recommendedSequenceAlterationClass ;
  owl:equivalentProperty vcfc:recommendedSequenceAlterationClass .

vcfr:recordId a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:recordId ;
  owl:equivalentProperty vcfc:recordId .

vcfr:ref a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:ref ;
  owl:equivalentProperty vcfc:ref .

vcfr:referenceGenome a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:referenceGenome ;
  owl:equivalentProperty vcfc:referenceGenome .

vcfr:ReferenceHeaderLine a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:ReferenceHeaderLine ;
  owl:equivalentClass vcfc:ReferenceHeaderLine .

vcfr:RepresentationProfile a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:RepresentationProfile ;
  owl:equivalentClass vcfc:RepresentationProfile .

vcfr:representationProfile a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:representationProfile ;
  owl:equivalentProperty vcfc:representationProfile .

vcfr:SampleCall a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:SampleCall ;
  owl:equivalentClass vcfc:SampleCall .

vcfr:sampleDataRaw a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:sampleDataRaw ;
  owl:equivalentProperty vcfc:sampleDataRaw .

vcfr:sampleId a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:sampleId ;
  owl:equivalentProperty vcfc:sampleId .

vcfr:sampleIndex a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:sampleIndex ;
  owl:equivalentProperty vcfc:sampleIndex .

vcfr:sampleName a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:sampleName ;
  owl:equivalentProperty vcfc:sampleName .

vcfr:SampleSet a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:SampleSet ;
  owl:equivalentClass vcfc:SampleSet .

vcfr:SourceHeaderLine a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:SourceHeaderLine ;
  owl:equivalentClass vcfc:SourceHeaderLine .

vcfr:sourceSoftware a owl:DatatypeProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:sourceSoftware ;
  owl:equivalentProperty vcfc:sourceSoftware .

# Was owl:Class in 1.1.0; vcfc:StringType became a named individual of
# vcfc:VCFValueType in 2.0.0, so the bridge is owl:sameAs, not
# owl:equivalentClass, which would no longer be OWL 2 DL.
vcfr:StringType a owl:NamedIndividual ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:StringType ;
  owl:sameAs vcfc:StringType .

vcfr:valueEncoding a owl:ObjectProperty ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:valueEncoding ;
  owl:equivalentProperty vcfc:valueEncoding .

vcfr:VariantCall a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:VariantCall ;
  owl:equivalentClass vcfc:VariantCall .

vcfr:VCFFile a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:VCFFile ;
  owl:equivalentClass vcfc:VCFFile .

vcfr:VCFHeader a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:VCFHeader ;
  owl:equivalentClass vcfc:VCFHeader .

vcfr:VCFNumberArity a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:VCFNumberArity ;
  owl:equivalentClass vcfc:VCFNumberArity .

vcfr:VCFRecord a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:VCFRecord ;
  owl:equivalentClass vcfc:VCFRecord .

vcfr:VCFSample a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:VCFSample ;
  owl:equivalentClass vcfc:VCFSample .

vcfr:VCFTextVector a owl:NamedIndividual ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:VCFTextVector ;
  owl:sameAs vcfc:VCFTextVector .

vcfr:VCFValueType a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:VCFValueType ;
  owl:equivalentClass vcfc:VCFValueType .

vcfr:VectorEncoding a owl:Class ;
  owl:deprecated true ;
  dct:isReplacedBy vcfc:VectorEncoding ;
  owl:equivalentClass vcfc:VectorEncoding .