VCF Core logo VCF Core Vocabulary https://w3id.org/vcf-core/vocab#

Vocabulary Reference

Class Hierarchy

This hierarchy summarizes the core design: file/header representation, record/call structure, expanded and condensed cohort genotype data, and typed definitions for INFO/FORMAT/FILTER/ALT metadata.

31 major branches|61 representative terms|24 structural links

Key Structural Relationships

Classes

Declared ontology terms extracted from the configured primary source file.

Term Label Relationships Description
vcfc:Allele VCF allele No graph relationships emitted An ordered allele participating in one VCF record. alleleIndex is 0 for REF and one-based for ALT, making VCF Number=A and Number=R values directly joinable without parsing the ALT string.
vcfc:AlleleKind VCF allele kind No graph relationships emitted A controlled syntactic category for an allele lexical form.
vcfc:AltAllele alternate allele Subclass Of: vcfc:Allele One ordered ALT allele, identified by a positive alleleIndex in source ALT order.
vcfc:AltDefinition ALT definition Subclass Of: vcfc:FieldDefinition The definition of one symbolic ALT identifier. It provides the meaning of an angle-bracketed alternate allele such as '<DEL>' without asserting a particular variation model.
vcfc:ALTHeaderLine ALT header line Subclass Of: vcfc:StructuredHeaderLine | Subclass Of: vcfc:AltDefinition A structured '##ALT=<...>' declaration that defines the meaning of a symbolic alternate-allele identifier. The identifier is used in the ALT column inside angle brackets, for example '<DEL>'.
vcfc:AssemblyContig breakpoint-assembly contig No graph relationships emitted A contig held in the external breakpoint-assembly file named by a '##assembly' line, referenced from CHROM as an angle-bracketed ID such as '<asm1>'. VCF 4.5 fixed field 1 admits this form as an alternative to a reference-sequence name. It is deliberately not a vcfc:ContigHeaderLine: no '##contig' declaration exists for it, and modelling it as one would assert a reference-sequence declaration the file does not make.
vcfc:AssemblyHeaderLine assembly header line Subclass Of: vcfc:UnstructuredHeaderLine The optional ##assembly line that locates a FASTA file containing breakpoint assemblies referenced by BKPTID.
vcfc:BaseModification base modification No graph relationships emitted A parsed base-modification carrier for VCF Number=M FORMAT fields. modifiedResidue links directly to the corresponding ChEBI resource; FALDO ForwardStrandPosition, ReverseStrandPosition, and BothStrandsPosition express the VCF strandedness convention without new VCF terms.
vcfc:Breakend breakend Subclass Of: vcfc:AltAllele A parsed bracketed VCF ALT allele representing a novel adjacency or terminus. The source expression remains in alleleValue.
vcfc:BreakendOrientation breakend orientation No graph relationships emitted One of the four bracket placements permitted by VCF breakend notation.
vcfc:CohortCallMatrix cohort call matrix Subclass Of: prov:Entity Added in version 1.1.0. A condensed representation of all sample genotype data for one VariantCall. It applies to exactly one ordered SampleSet and groups one FormatValueVector for each represented FORMAT key. A matrix does not itself assert an individual RDF statement for every sample value.
vcfc:ColumnHeaderLine column header line No graph relationships emitted The mandatory tab-delimited #CHROM line. It declares the eight fixed VCF columns and, where genotype data occur, FORMAT followed by ordered sample columns. It is distinct from a ## meta-information HeaderLine.
vcfc:ConfidenceInterval confidence interval No graph relationships emitted A lower and upper VCF interval for CILEN, CICN, CIRUC, or CIRB. CILEN contains length bounds, not POS offsets. CIPOS and CIEND instead use FALDO InRangePosition.
vcfc:ContigHeaderLine contig header line Subclass Of: vcfc:StructuredHeaderLine A structured '##contig=<...>' declaration for a reference sequence used by records in the file. VCF 4.5 requires its ID and reserves optional attributes such as length, md5, and URL; contig declarations are recommended in VCF and required in BCF.
vcfc:EventType event type No graph relationships emitted A reserved VCF EVENTTYPE code.
vcfc:FieldDefinition field definition No graph relationships emitted A reusable specification- or file-level definition of an INFO, FORMAT, FILTER, ALT, or META key. It is not itself a VCF header line: a concrete file declaration uses the corresponding *HeaderLine subclass.
vcfc:FieldValueItem field value item No graph relationships emitted One ordered, parsed item from the comma-separated payload of an INFO or FORMAT field. The parent field value retains the original lexical payload for round-tripping.
vcfc:FileDateHeaderLine fileDate header line Subclass Of: vcfc:UnstructuredHeaderLine An optional producer-supplied '##fileDate' meta-information line. It is a commonly used unstructured header convention, rather than a required VCF 4.5 line.
vcfc:FileFormatHeaderLine fileformat header line Subclass Of: vcfc:UnstructuredHeaderLine The required, first VCF meta-information line. Its value declares the VCF version, for example 'VCFv4.5'.
vcfc:FilterCode filter failure code No graph relationships emitted One failed FILTER or FT code. PASS and missing are statuses, not failure codes.
vcfc:FilterDefinition FILTER definition Subclass Of: vcfc:FieldDefinition The definition of one FILTER failure code. A VCF record that fails this criterion cites the code in its semicolon-separated FILTER value.
vcfc:FILTERHeaderLine FILTER header line Subclass Of: vcfc:StructuredHeaderLine | Subclass Of: vcfc:FilterDefinition A structured '##FILTER=<...>' declaration that defines a code which may appear in the FILTER column when a record does not pass that filter. ID and Description are required by VCF 4.5.
vcfc:FilterStatus filter status No graph relationships emitted -
vcfc:FormatFieldDefinition FORMAT field definition Subclass Of: vcfc:FieldDefinition The definition of one FORMAT key, including its ID, Number, Type, and human-readable Description. It specifies how the corresponding per-sample values must be interpreted. Since version 1.1.0, it can also declare a condensed vcfc:FormatValueVector through vcfc:declaredBy.
vcfc:FormatFieldValue FORMAT field value No graph relationships emitted A structured representation of one value from one sample's colon-delimited data block, interpreted at the corresponding position in the record's FORMAT key list. This is an expanded, per-sample resource; version 1.1.0 added vcfc:FormatValueVector for a condensed multi-sample representation and the two classes MUST NOT be substituted for one another.
vcfc:FORMATHeaderLine FORMAT header line Subclass Of: vcfc:StructuredHeaderLine | Subclass Of: vcfc:FormatFieldDefinition A structured '##FORMAT=<...>' declaration that defines the identifier, cardinality, type, and meaning of a field in a per-sample column. ID, Number, Type, and Description are required by VCF 4.5.
vcfc:FormatKey declared FORMAT key No graph relationships emitted One key of one record's FORMAT column, in column order. VCF 4.5 lets a sample drop trailing fields, so the keys a record declares and the values a sample supplies are different sets. Without this resource the declared list exists only inside the vcfc:formatRaw string, and a consumer could not tell an omitted field from an undeclared one without parsing it.
vcfc:FormatValueVector FORMAT value vector Subclass Of: prov:Entity Added in version 1.1.0. The values of one FORMAT key across the ordered members of a CohortCallMatrix's SampleSet. It MUST be linked to the corresponding FormatFieldDefinition with vcfc:declaredBy and its encoded values MUST contain one position for each sample, including explicit missing values. It is a compact container, not a collection of individual vcfc:FormatFieldValue assertions.
vcfc:Genotype VCF genotype No graph relationships emitted The parsed GT field for one SampleCall. It preserves genotypeString and represents its ordered allele calls and phasing independently.
vcfc:GenotypeAlleleCall genotype allele call No graph relationships emitted One allele position in a parsed GT value. callIndex preserves genotype order; isNoCall represents a dot call without inventing an allele.
vcfc:HeaderAttribute header attribute No graph relationships emitted One key-value attribute from a structured VCF header line. It makes required, optional, and implementation-defined attributes queryable while headerValue retains the source form.
vcfc:HeaderLine VCF header line No graph relationships emitted A representation of one VCF meta-information line, such as '##fileformat=VCFv4.5' or '##INFO=<...>'. A line may have an unstructured value or a structured, angle-bracketed list of key-value pairs.
vcfc:InfoFieldDefinition INFO field definition Subclass Of: vcfc:FieldDefinition The definition of one INFO key, including its ID, Number, Type, and human-readable Description. It specifies how that key's site-level annotation values must be interpreted.
vcfc:InfoFieldValue INFO field value No graph relationships emitted A structured representation of one key and its optional value(s) from the INFO column of a VCF record. INFO entries are separated by semicolons, and an entry without an equals sign represents a Flag-style presence assertion.
vcfc:INFOHeaderLine INFO header line Subclass Of: vcfc:StructuredHeaderLine | Subclass Of: vcfc:InfoFieldDefinition A structured '##INFO=<...>' declaration that defines the identifier, cardinality, type, and meaning of an annotation that may occur in the INFO column. ID, Number, Type, and Description are required by VCF 4.5.
vcfc:LocalAlleleMembership local allele membership No graph relationships emitted An ordered membership in one sample's LocalAlleleSet. The membership, rather than the shared ALT allele, carries the local index.
vcfc:LocalAlleleSet local allele set No graph relationships emitted The subset of ALT alleles declared as locally relevant to a sample by LAA. Its members keep their record-global alleleIndex values.
vcfc:MetaDefinition META definition Subclass Of: vcfc:FieldDefinition A ##META declaration represented as a reusable field definition. Its fieldId, fieldArity, and fieldType describe attributes used on ##SAMPLE lines.
vcfc:MetaHeaderLine META header line Subclass Of: vcfc:StructuredHeaderLine | Subclass Of: vcfc:MetaDefinition A structured ##META declaration that defines an implementation- or file-specific sample attribute key and optional allowed values.
vcfc:PaddingInterpretation padding-base interpretation No graph relationships emitted A derived statement about which base of a record's alleles serves as the VCF padding base, together with the specification rule that determined it. It never replaces or trims vcfc:ref and vcfc:alleleValue, which keep the source strings; a consumer that ignores this resource still sees the record exactly as written.
vcfc:PaddingRule padding rule No graph relationships emitted The VCF 4.5 provision under which a padding interpretation was derived. Naming the rule keeps the interpretation auditable and makes the undetermined case explicit rather than silent.
vcfc:PaddingSide padding side No graph relationships emitted Whether the padding base precedes or follows the variant bases.
vcfc:PedigreeDBHeaderLine pedigreeDB header line Subclass Of: vcfc:UnstructuredHeaderLine The optional ##pedigreeDB line that identifies an external pedigree database.
vcfc:PedigreeHeaderLine PEDIGREE header line Subclass Of: vcfc:StructuredHeaderLine | Subclass Of: vcfc:PedigreeRelation A structured ##PEDIGREE declaration. Its HeaderAttribute resources retain arbitrary ancestor-role attributes; pedigreeMother and pedigreeFather provide direct links when those roles are represented as resources.
vcfc:PedigreeRelation pedigree relation No graph relationships emitted A parent, ancestor, or clonal-origin relationship declared in VCF pedigree metadata.
vcfc:PhaseSet phase set No graph relationships emitted A parsed phase-set identifier or list carried by PS or PSL, optionally with PSO and PSQ information.
vcfc:PhasingStatus phasing status No graph relationships emitted The separator semantics between genotype allele calls.
vcfc:RecordIdentifier record identifier No graph relationships emitted One component of the semicolon-separated ID column. The missing dot is represented by no identifier components.
vcfc:ReferenceAllele reference allele Subclass Of: vcfc:Allele The record's REF allele, identified by alleleIndex 0.
vcfc:ReferenceBlock reference block No graph relationships emitted A reference interval for one sample, linked to its unspecified ALT allele with blockAllele. Different samples may have different FORMAT LEN extents for the same record.
vcfc:ReferenceHeaderLine reference header line Subclass Of: vcfc:UnstructuredHeaderLine An optional '##reference' meta-information line that identifies the reference genome or sequence resource used to interpret the records. Including reference and contig metadata is recommended by VCF 4.5.
vcfc:RepeatSequence repeat sequence No graph relationships emitted One repeat sequence within a tandem-repeat allele, indexed in VCF RN/RUS/RUL/RUC/RB order.
vcfc:RepeatUnit repeat unit No graph relationships emitted One individually sized repeat unit used only when RUB distinguishes varying unit lengths.
vcfc:RepresentationProfile VCF RDF representation profile No graph relationships emitted Added in version 1.1.0. A declared profile that tells consumers whether genotype data are emitted as individual expanded statements or as condensed, sample-ordered vectors.
vcfc:SampleCall sample call Subclass Of: prov:Entity The colon-delimited value block for one sample in a genotype-bearing VCF record, represented as structured FORMAT field values. Its field order and meanings are supplied by that record's FORMAT column and corresponding FORMAT declarations. This is the expanded representation retained for single-sample and low-sample VCF files; it MUST NOT be used to represent a vector of values for multiple samples.
vcfc:SampleDeclaration sample declaration Subclass Of: prov:Entity The declared subject of one ##SAMPLE header line. This is a header-level declaration and is distinct from a VCFSample, which identifies a #CHROM sample column.
vcfc:SampleHeaderLine SAMPLE header line Subclass Of: vcfc:StructuredHeaderLine A structured ##SAMPLE declaration describing a sample or genome mapping through standard or META-declared attributes.
vcfc:SampleSet VCF sample set Subclass Of: prov:Entity Added in version 1.1.0. The ordered set of sample columns declared by one VCF file. The vcfc:sampleIndex of each member is one-based and determines how values in a condensed representation are associated with samples.
vcfc:SourceHeaderLine source header line Subclass Of: vcfc:UnstructuredHeaderLine An optional producer-supplied '##source' meta-information line, typically identifying the program, pipeline, or source that generated the VCF.
vcfc:StructuredHeaderLine structured header line Subclass Of: vcfc:HeaderLine A VCF meta-information line whose value is an angle-bracketed, comma-separated list of key-value attributes. Implementations must not rely on the source attribute order, but may preserve it with vcfc:attributeIndex.
vcfc:SVClaim structural-variant claim No graph relationships emitted The per-ALT SVCLAIM code indicating an abundance claim, adjacency claim, or both.
vcfc:SymbolicAlleleType symbolic allele type No graph relationships emitted A reserved first-level symbolic ALT type or recommended subtype. It represents VCF syntax and points outward to SO rather than reclassifying an allele as an SO entity.
vcfc:TandemRepeatAllele tandem-repeat allele Subclass Of: vcfc:AltAllele A <CNV:TR> alternate allele whose repeat sequences and units are represented through the VCF tandem-repeat fields.
vcfc:UnstructuredHeaderLine unstructured header line Subclass Of: vcfc:HeaderLine A VCF meta-information line whose non-empty value is not an angle-bracketed attribute list.
vcfc:VariantCall variant call Subclass Of: prov:Entity A vocabulary-level resource that groups the call assessment carried by a VCF record: QUAL, FILTER, INFO, the FORMAT declaration, and sample genotype data. It is an RDF convenience for the contents of a record, not a separate line type in VCF syntax. Since version 1.1.0, genotype data can be represented either as expanded per-sample calls or through one condensed cohort call matrix.
vcfc:VariantEvent variant event No graph relationships emitted A named EVENT grouping records that jointly describe a complex rearrangement or another related variation event.
vcfc:VCF41File VCF 4.1 file Subclass Of: vcfc:VCFFile An optional explicit VCF 4.1 file type. Use it when the VCF 4.1 SHACL version gate is wanted; VCFFile itself remains version-neutral, and the matching overlay also scopes its rules by fileFormat.
vcfc:VCF42File VCF 4.2 file Subclass Of: vcfc:VCFFile An optional explicit VCF 4.2 file type. Use it when the VCF 4.2 SHACL version gate is wanted; VCFFile itself remains version-neutral, and the matching overlay also scopes its rules by fileFormat.
vcfc:VCF43File VCF 4.3 file Subclass Of: vcfc:VCFFile An optional explicit VCF 4.3 file type. Use it when the VCF 4.3 SHACL version gate is wanted; VCFFile itself remains version-neutral, and the matching overlay also scopes its rules by fileFormat.
vcfc:VCF44File VCF 4.4 file Subclass Of: vcfc:VCFFile An optional explicit VCF 4.4 file type. Use it when the VCF 4.4 SHACL version gate is wanted; VCFFile itself remains version-neutral, and the matching overlay also scopes its rules by fileFormat.
vcfc:VCF45File VCF 4.5 file Subclass Of: vcfc:VCFFile An optional explicit VCF 4.5 file type. Use it when the VCF 4.5 SHACL version gate is wanted; VCFFile itself remains version-neutral, and the matching overlay also scopes its rules by fileFormat.
vcfc:VCFFile VCF file Subclass Of: dcat:Distribution | Subclass Of: prov:Entity A Variant Call Format (VCF) file artifact represented as a dataset distribution. In VCF 4.5, the artifact contains meta-information lines, one column-header line, and zero or more tab-delimited data records.
vcfc:VCFHeader VCF header No graph relationships emitted A resource that groups the VCF file's meta-information header lines. VCF 4.5 meta-information lines begin with '##' and occur before the mandatory '#CHROM' column-header line and all data records.
vcfc:VCFNumberArity VCF Number arity No graph relationships emitted The cardinality declaration used in a structured INFO or FORMAT definition. Besides a non-negative integer, VCF 4.5 defines A (one value per ALT allele), R (one per allele including REF), G (one per genotype), and '.' (variable, unknown, or unbounded); FORMAT additionally defines LA, LR, LG, P, and M.
vcfc:VCFRecord VCF record Subclass Of: prov:Entity One tab-delimited VCF data line. It contains the eight mandatory fixed fields CHROM, POS, ID, REF, ALT, QUAL, FILTER, and INFO; it may additionally contain a FORMAT field and one value block per sample. This is a VCF-centric representation that can link to a sequence-alteration model via vcfc:asSequenceAlteration.
vcfc:VCFSample VCF sample Subclass Of: prov:Entity Added in version 1.1.0. A reusable representation of one named sample column in one VCF file. It identifies a VCF column, not necessarily a biological individual; external subject or biosample resources may be linked separately.
vcfc:VCFValueType VCF value type No graph relationships emitted The declared VCF data type of an INFO or FORMAT field. INFO definitions may use Integer, Float, Flag, Character, or String; FORMAT definitions may use all of these except Flag.
vcfc:VectorEncoding FORMAT value vector encoding No graph relationships emitted Added in version 1.1.0. A named encoding for the lexical payload of a FormatValueVector. The encoding is required to interpret vcfc:encodedValues.

Object Properties

Declared ontology terms extracted from the configured primary source file.

Term Label Relationships Description
vcfc:alleleKind allele kind Domain: vcfc:Allele | Range: vcfc:AlleleKind -
vcfc:allelePhaseSet allele phase set Domain: vcfc:GenotypeAlleleCall | Range: vcfc:PhaseSet The PSL entry for this GT allele call; missing entries have no link.
vcfc:appliesToSampleSet applies to sample set Domain: vcfc:CohortCallMatrix | Range: vcfc:SampleSet Added in version 1.1.0. Identifies the ordered SampleSet used to interpret a CohortCallMatrix and all of its FORMAT value vectors.
vcfc:asSequenceAlteration as sequence alteration Range: so:0001059 Links the VCF-centric record or call to an independently modelled sequence alteration, such as an SB/gvar SequenceAlteration. This relation supports semantic alignment without changing the source VCF representation.
vcfc:blockAllele block allele Domain: vcfc:ReferenceBlock | Range: vcfc:AltAllele -
vcfc:breakendOrientation breakend orientation Domain: vcfc:Breakend | Range: vcfc:BreakendOrientation -
vcfc:calledAllele called allele Domain: vcfc:GenotypeAlleleCall | Range: vcfc:Allele -
vcfc:chromAssemblyContig CHROM assembly contig Domain: vcfc:VCFRecord | Range: vcfc:AssemblyContig Associates a record whose CHROM is an angle-bracketed assembly-contig ID with that contig. It is the structured counterpart of vcfc:chromosome, which links a record to a declared reference contig; a record uses one or the other, never both.
vcfc:chromosome chromosome / contig reference Domain: vcfc:VCFRecord | Range: vcfc:ContigHeaderLine Links a record to the declared contig corresponding to its CHROM value. The CHROM column identifies a reference sequence (or, for breakpoint assemblies, an angle-bracketed assembly contig ID); a resolvable external reference may also be aligned to FALDO.
vcfc:copyNumberConfidenceInterval copy-number confidence interval Range: vcfc:ConfidenceInterval -
vcfc:declaredBy declared by Range: vcfc:FieldDefinition Links an INFO, FORMAT, FILTER, or ALT value/usage to its header definition line. Since version 1.1.0, a FormatValueVector uses this property to identify the FORMAT key that defines every position in the vector.
vcfc:declaredByAlt declared by ALT definition Domain: vcfc:AltAllele | Range: vcfc:AltDefinition -
vcfc:declaredByFilter declared by filter Domain: vcfc:FilterCode | Range: vcfc:FilterDefinition -
vcfc:declaredInAssembly declared in assembly file Domain: vcfc:AssemblyContig | Range: vcfc:AssemblyHeaderLine Links a breakpoint-assembly contig to the '##assembly' header line whose URL names the file that holds its sequence. This is the contig's sequence source; the vocabulary does not fetch or model the sequence itself.
vcfc:declaredOnLine declared on header line Domain: vcfc:FieldDefinition | Range: vcfc:HeaderLine Links a reusable field definition to the concrete HeaderLine that declares it in one VCF file. This keeps specification-level registry definitions distinct from file-local header-line occurrences.
vcfc:declaresSample declares sample Domain: vcfc:SampleHeaderLine | Range: vcfc:SampleDeclaration -
vcfc:endConfidenceInterval END confidence interval Domain: vcfc:AltAllele | Range: faldo:InRangePosition Represents CIEND through FALDO InRangePosition rather than a VCF-specific ConfidenceInterval.
vcfc:eventType event type Domain: vcfc:VariantEvent | Range: vcfc:EventType -
vcfc:fieldArity field arity Domain: vcfc:FieldDefinition | Range: vcfc:VCFNumberArity Links a field definition with a symbolic VCF Number arity. For a fixed count, use fieldNumberInteger; fieldNumber always preserves the exact source token.
vcfc:fieldType field Type Domain: vcfc:FieldDefinition | Range: vcfc:VCFValueType Links an INFO or FORMAT field declaration to its VCF Type. INFO supports Integer, Float, Flag, Character, and String; FORMAT supports all of those except Flag.
vcfc:filterStatus filter status Range: vcfc:FilterStatus Status of FILTER on a VariantCall or FT on a SampleCall.
vcfc:forAllele for allele Domain: vcfc:FieldValueItem | Range: vcfc:Allele -
vcfc:forBaseModification for base modification Domain: vcfc:FieldValueItem Links a Number=M value item to the applicable BaseModification resource when that layer is used.
vcfc:forSample for sample Domain: vcfc:SampleCall | Range: vcfc:VCFSample Added in version 1.1.0. Optionally links an expanded SampleCall to the reusable VCFSample representing its column. This avoids treating repeated vcfc:sampleId literals as the only sample identity.
vcfc:hasAlleleCall has allele call Domain: vcfc:Genotype | Range: vcfc:GenotypeAlleleCall -
vcfc:hasAltAllele has alternate allele Domain: vcfc:VCFRecord | Range: vcfc:AltAllele -
vcfc:hasAttribute has attribute Domain: vcfc:StructuredHeaderLine | Range: vcfc:HeaderAttribute -
vcfc:hasCall has call Domain: vcfc:VCFRecord | Range: vcfc:VariantCall Associates a VCF record with its vocabulary-level call resource, which groups QUAL, FILTER, INFO, FORMAT, and per-sample call data.
vcfc:hasCallMatrix has cohort call matrix Domain: vcfc:VariantCall | Range: vcfc:CohortCallMatrix Added in version 1.1.0. Associates a VariantCall with its condensed multi-sample genotype representation. It is the condensed-profile alternative to emitting one vcfc:hasSampleCall assertion per sample.
vcfc:hasColumnHeader has column header Domain: vcfc:VCFHeader | Range: vcfc:ColumnHeaderLine -
vcfc:hasFilterCode has filter failure code Range: vcfc:FilterCode -
vcfc:hasFormatKey has declared FORMAT key Domain: vcfc:VariantCall | Range: vcfc:FormatKey Associates a record-level call with one key declared in its FORMAT column. The key's position comes from vcfc:fieldIndex and its meaning from vcfc:declaredBy, so the declared order is queryable without reading vcfc:formatRaw.
vcfc:hasFormatValue has FORMAT value Domain: vcfc:SampleCall | Range: vcfc:FormatFieldValue Associates a sample call with one structured value parsed from that sample's FORMAT-ordered data block.
vcfc:hasFormatValueVector has FORMAT value vector Domain: vcfc:CohortCallMatrix | Range: vcfc:FormatValueVector Added in version 1.1.0. Associates a CohortCallMatrix with the ordered values for one FORMAT key across its SampleSet.
vcfc:hasGenotype has genotype Domain: vcfc:SampleCall | Range: vcfc:Genotype -
vcfc:hasGenotypeColumns has genotype columns Domain: vcfc:ColumnHeaderLine | Range: vcfc:VCFSample -
vcfc:hasHeader has header Domain: vcfc:VCFFile | Range: vcfc:VCFHeader Associates a VCF file artifact with the resource that groups its meta-information header lines.
vcfc:hasHeaderLine has header line Domain: vcfc:VCFHeader | Range: vcfc:HeaderLine Associates a VCF header with one of its meta-information lines. This preserves the individual declaration even when its structured attributes are also represented separately.
vcfc:hasIdentifier has identifier Domain: vcfc:VCFRecord | Range: vcfc:RecordIdentifier -
vcfc:hasInfoValue has INFO value Domain: vcfc:VariantCall | Range: vcfc:InfoFieldValue Associates a record-level call with one structured annotation parsed from its INFO column.
vcfc:hasLocalAllele has local allele Domain: vcfc:LocalAlleleSet | Range: vcfc:AltAllele -
vcfc:hasLocalAlleleMembership has local allele membership Domain: vcfc:LocalAlleleSet | Range: vcfc:LocalAlleleMembership -
vcfc:hasLocalAlleleSet has local allele set Domain: vcfc:Genotype | Range: vcfc:LocalAlleleSet -
vcfc:hasPaddingInterpretation has padding interpretation Domain: vcfc:VCFRecord | Range: vcfc:PaddingInterpretation Associates a record with the padding interpretation derived for its alleles. At most one interpretation is asserted per record.
vcfc:hasRecord has record Domain: vcfc:VCFFile | Range: vcfc:VCFRecord Associates a VCF file with one of its tab-delimited data records.
vcfc:hasReferenceAllele has reference allele Domain: vcfc:VCFRecord | Range: vcfc:ReferenceAllele -
vcfc:hasReferenceBlock has reference block Range: vcfc:ReferenceBlock -
vcfc:hasRepeatSequence has repeat sequence Domain: vcfc:TandemRepeatAllele | Range: vcfc:RepeatSequence -
vcfc:hasRepeatUnit has repeat unit Domain: vcfc:RepeatSequence | Range: vcfc:RepeatUnit -
vcfc:hasSample has sample Domain: vcfc:SampleSet | Range: vcfc:VCFSample Added in version 1.1.0. Associates a SampleSet with a reusable VCF sample-column resource. The member's vcfc:sampleIndex supplies the set order.
vcfc:hasSampleCall has sample call Domain: vcfc:VariantCall | Range: vcfc:SampleCall Associates a record-level call with the values for one sample. It is used only when the VCF record includes genotype columns. This property is the expanded-profile alternative to vcfc:hasCallMatrix, not a link to a condensed vector.
vcfc:hasSampleSet has sample set Domain: vcfc:VCFFile | Range: vcfc:SampleSet Added in version 1.1.0. Associates a VCF file with its ordered set of sample columns. The set provides the sample order used by every condensed cohort call matrix in that file.
vcfc:hasValueItem has value item Range: vcfc:FieldValueItem -
vcfc:inEvent in event Range: vcfc:VariantEvent -
vcfc:inPhaseSet in phase set Domain: vcfc:Genotype | Range: vcfc:PhaseSet -
vcfc:lenConfidenceInterval SVLEN confidence interval Domain: vcfc:AltAllele | Range: vcfc:ConfidenceInterval -
vcfc:localAllele local allele Domain: vcfc:LocalAlleleMembership | Range: vcfc:AltAllele -
vcfc:mateBreakend mate breakend Domain: vcfc:Breakend | Range: vcfc:Breakend -
vcfc:modifiedResidue modified residue Domain: vcfc:BaseModification Links directly to the ChEBI class denoting the modified residue.
vcfc:paddingRule padding rule Domain: vcfc:PaddingInterpretation | Range: vcfc:PaddingRule The specification provision that produced this padding interpretation.
vcfc:paddingSide padding side Domain: vcfc:PaddingInterpretation | Range: vcfc:PaddingSide Which side of the variant bases the padding base occupies. Asserted only when a padding rule determines it.
vcfc:partnerBreakend partner breakend Domain: vcfc:Breakend | Range: vcfc:Breakend -
vcfc:pedigreeAncestor pedigree ancestor Domain: vcfc:PedigreeRelation | Range: vcfc:SampleDeclaration -
vcfc:pedigreeFather pedigree father Domain: vcfc:PedigreeRelation | Range: vcfc:SampleDeclaration -
vcfc:pedigreeMother pedigree mother Domain: vcfc:PedigreeRelation | Range: vcfc:SampleDeclaration -
vcfc:pedigreeOriginal pedigree original Domain: vcfc:PedigreeRelation | Range: vcfc:SampleDeclaration The clonal Original= relation in a ##PEDIGREE line. It is explicitly a PROV derivation relation; parent and generic ancestor links are not globally forced to that interpretation.
vcfc:phasingStatus phasing status Domain: vcfc:Genotype | Range: vcfc:PhasingStatus -
vcfc:posConfidenceInterval POS confidence interval Domain: vcfc:AltAllele | Range: faldo:InRangePosition Represents CIPOS through FALDO InRangePosition rather than a VCF-specific ConfidenceInterval.
vcfc:rbConfidenceInterval RB confidence interval Domain: vcfc:RepeatSequence | Range: vcfc:ConfidenceInterval -
vcfc:representationProfile representation profile Domain: vcfc:VCFFile | Range: vcfc:RepresentationProfile Added in version 1.1.0. Declares the genotype-data representation used by a VCF RDF graph. A converter MUST use vcfc:ExpandedRepresentation when emitting per-sample call resources and vcfc:CondensedRepresentation when emitting cohort call matrices.
vcfc:rucConfidenceInterval RUC confidence interval Domain: vcfc:RepeatSequence | Range: vcfc:ConfidenceInterval -
vcfc:svClaim SV claim Domain: vcfc:AltAllele | Range: vcfc:SVClaim -
vcfc:svSubtypeOf SV subtype of Domain: vcfc:SymbolicAlleleType | Range: vcfc:SymbolicAlleleType -
vcfc:svType SV type Domain: vcfc:AltAllele | Range: vcfc:SymbolicAlleleType -
vcfc:valueEncoding value encoding Domain: vcfc:FormatValueVector | Range: vcfc:VectorEncoding Added in version 1.1.0. Names the lexical encoding used for a FormatValueVector's vcfc:encodedValues payload.

Datatype Properties

Declared ontology terms extracted from the configured primary source file.

Term Label Relationships Description
vcfc:alleleIndex allele index Domain: vcfc:Allele | Range: xsd:nonNegativeInteger -
vcfc:alleleValue allele value Domain: vcfc:Allele | Range: rdfs:Literal -
vcfc:alt ALT Domain: vcfc:VCFRecord | Range: xsd:string A lossless raw ALT lexical value. The VCF source serializes ALT as an ordered comma-separated list whose items may be base strings, '*', '.', symbolic IDs, '<*>', or breakend expressions. Repeated vcfc:alt assertions are unsuitable for per-allele annotation or preserving ALT order; use hasAltAllele and alleleIndex for the structural form.
vcfc:altId ALT ID Domain: vcfc:AltDefinition | Range: xsd:string The ID of a symbolic ALT declaration, stored without the angle brackets used when the identifier occurs in the ALT column.
vcfc:ancestorRole ancestor role Domain: vcfc:PedigreeRelation | Range: xsd:string -
vcfc:ancestralHaplotypeId ancestral haplotype ID Domain: vcfc:SampleCall | Range: xsd:integer -
vcfc:arityCode arity code Domain: vcfc:VCFNumberArity | Range: xsd:string -
vcfc:assemblyContigId assembly contig ID Domain: vcfc:AssemblyContig | Range: xsd:string The identifier of a breakpoint-assembly contig with the angle brackets removed, so that '<asm1>' in CHROM yields 'asm1'. The bracketed source token stays available on vcfc:chrom.
vcfc:assemblyUrl assembly URL Domain: vcfc:AssemblyHeaderLine | Range: xsd:anyURI -
vcfc:attributeIndex attribute index Domain: vcfc:HeaderAttribute | Range: xsd:positiveInteger -
vcfc:attributeKey attribute key Domain: vcfc:HeaderAttribute | Range: xsd:string -
vcfc:attributeValue attribute value Domain: vcfc:HeaderAttribute | Range: xsd:string -
vcfc:breakendReplacementString breakend replacement string Domain: vcfc:Breakend | Range: vcfc:BreakendString -
vcfc:callIndex allele-call index Domain: vcfc:GenotypeAlleleCall | Range: xsd:nonNegativeInteger -
vcfc:chrom CHROM Domain: vcfc:VCFRecord | Range: xsd:string The required CHROM fixed-field value: an identifier for the reference sequence on which the record is located, or an angle-bracketed assembly-contig ID for a breakpoint assembly. Records for one CHROM occur in a contiguous block.
vcfc:ciLower confidence-interval lower bound Domain: vcfc:ConfidenceInterval | Range: rdfs:Literal -
vcfc:ciUpper confidence-interval upper bound Domain: vcfc:ConfidenceInterval | Range: rdfs:Literal -
vcfc:componentIndex component index Range: xsd:positiveInteger One-based position of an ID or FILTER component in its source column.
vcfc:contigAssembly contig assembly Domain: vcfc:ContigHeaderLine | Range: xsd:string An optional assembly identifier supplied in a contig declaration. It identifies the reference assembly context for the named contig.
vcfc:contigCount contig count Domain: vcfc:VCFFile | Range: xsd:integer The number of contig declarations associated with the file. This is a derived RDF convenience, not a separate VCF header field.
vcfc:contigId contig ID Domain: vcfc:ContigHeaderLine | Range: xsd:string The required ID attribute of a '##contig=<...>' declaration. It names the reference sequence that may be cited in CHROM and must not be a reserved symbolic-allele name.
vcfc:contigLength contig length Domain: vcfc:ContigHeaderLine | Range: xsd:integer The optional 'length' attribute of a contig declaration: the length of the reference sequence in bases.
vcfc:contigMd5 contig MD5 Domain: vcfc:ContigHeaderLine | Range: xsd:string The optional 'md5' attribute of a contig declaration: the lowercase hexadecimal MD5 checksum of the normalized reference sequence, as defined by the SAM specification and referenced by VCF 4.5.
vcfc:contigUrl contig URL Domain: vcfc:ContigHeaderLine | Range: xsd:anyURI -
vcfc:copyNumber copy number Range: rdfs:Literal -
vcfc:copyNumberLikelihood copy-number likelihood Domain: vcfc:SampleCall | Range: rdfs:Literal -
vcfc:copyNumberPosterior copy-number posterior Domain: vcfc:SampleCall | Range: rdfs:Literal -
vcfc:copyNumberQuality copy-number quality Domain: vcfc:SampleCall | Range: rdfs:Literal -
vcfc:decodedValue decoded value Range: rdfs:Literal A consumer-oriented value after applying the file's percent-encoding policy; rawValue remains authoritative for round-tripping.
vcfc:encodedValues encoded values Domain: vcfc:FormatValueVector | Range: xsd:string Added in version 1.1.0. The lexical payload of a FormatValueVector. Interpret it only according to vcfc:valueEncoding, the vector's vcfc:declaredBy FORMAT definition, and the SampleSet of its CohortCallMatrix; it is not a sequence of independently asserted RDF values.
vcfc:endPosition end position Domain: vcfc:ReferenceBlock | Range: xsd:integer -
vcfc:eventTypeCode event type code Domain: vcfc:EventType | Range: xsd:string -
vcfc:fieldDescription field Description Domain: vcfc:FieldDefinition | Range: xsd:string The human-readable Description attribute from a structured INFO, FORMAT, FILTER, or ALT header declaration. VCF requires this attribute to be quoted in the source header.
vcfc:fieldId field ID Domain: vcfc:FieldDefinition | Range: xsd:string The ID attribute of an INFO or FORMAT field declaration. It is the key used to identify a value in the INFO column or FORMAT-ordered sample data and is unique within its header-line type.
vcfc:fieldIndex field index Range: xsd:positiveInteger One-based source order of an INFO entry or FORMAT field value within its parent.
vcfc:fieldNumber field Number Domain: vcfc:FieldDefinition | Range: xsd:string The Number attribute from an INFO or FORMAT definition, retained as a string because VCF permits both integers and symbolic arities. A, R, and G follow REF/ALT or genotype order; '.' means variable, unknown, or unbounded; FORMAT also permits LA, LR, LG, P, and M.
vcfc:fieldNumberInteger field Number integer Domain: vcfc:FieldDefinition | Range: xsd:nonNegativeInteger -
vcfc:fieldSource field source Domain: vcfc:INFOHeaderLine | Range: xsd:string -
vcfc:fieldValue field value Range: rdfs:Literal The literal value copied from one structured INFO or FORMAT entry. It may preserve a comma-separated VCF value list; when a source value is missing, use '.'^^vcfc:Null. The typed value properties may additionally be used where the source type and transformation support them. In the version 1.1.0 condensed profile, use vcfc:encodedValues on a FormatValueVector instead of creating one vcfc:fieldValue assertion per sample.
vcfc:fieldValueBoolean field value (boolean) Range: xsd:boolean An RDF boolean representation that may be used for the presence semantics of a VCF INFO Flag. In VCF source syntax, a Flag is indicated by a key without an explicit value and has Number=0.
vcfc:fieldValueDecimal field value (decimal) Range: xsd:decimal An RDF decimal representation of a parsed finite VCF Float field value. VCF Float may also use INF, INFINITY, or NAN; preserve such lexical values with vcfc:fieldValue rather than coercing them to xsd:decimal.
vcfc:fieldValueInteger field value (integer) Range: xsd:integer An RDF integer representation of a parsed VCF Integer field value. Use vcfc:fieldValue for the original lexical form, lists, or missing values.
vcfc:fieldVersion field version Domain: vcfc:INFOHeaderLine | Range: xsd:string -
vcfc:fileDate file date Domain: vcfc:VCFFile | Range: xsd:date A producer-supplied file date, typically derived from an optional '##fileDate' header line. It records file metadata and is not one of VCF 4.5's required fixed fields.
vcfc:fileFormat file format Domain: vcfc:VCFFile | Range: xsd:string The VCF version string declared by the required '##fileformat' line, for example 'VCFv4.5'. That line must be the first line of a conforming VCF file.
vcfc:filter FILTER Domain: vcfc:VariantCall | Range: rdfs:Literal The FILTER fixed-field value. 'PASS' means the position passed all filters; otherwise it is a semicolon-separated list of declared filter codes that failed. '.'^^vcfc:Null means filters have not been applied.
vcfc:filterCodeValue filter code value Domain: vcfc:FilterCode | Range: xsd:string -
vcfc:filterId FILTER ID Domain: vcfc:FilterDefinition | Range: xsd:string The ID of a FILTER declaration: the failure code that can occur in the semicolon-separated FILTER column when the corresponding criterion is not passed.
vcfc:forGenotypeIndex for genotype index Domain: vcfc:FieldValueItem | Range: xsd:nonNegativeInteger -
vcfc:forGTAlleleIndex for GT allele index Domain: vcfc:FieldValueItem | Range: xsd:nonNegativeInteger -
vcfc:formatRaw FORMAT raw Domain: vcfc:VariantCall | Range: xsd:string An optional lossless copy of the FORMAT column: the colon-separated, ordered list of keys that determines the meaning of every sample data block in the record. If GT is included, it is the first key; the same field order applies to all samples in the record. Since version 1.1.0, this order also determines how a condensed CohortCallMatrix's FORMAT value vectors are combined for a sample.
vcfc:genotypeIndex genotype index Range: xsd:nonNegativeInteger The VCF Number=G index for genotype alleles k₁…k_P: Index(k₁…k_P) = Σ C(k_m + m − 1, m).
vcfc:genotypeString genotype string Domain: vcfc:Genotype | Range: vcfc:GenotypeString -
vcfc:haplotypeId haplotype ID Domain: vcfc:SampleCall | Range: xsd:integer -
vcfc:headerKey header key Domain: vcfc:HeaderLine | Range: xsd:string The meta-information key to the left of '=' in a header line, without the leading '##'; for example, 'fileformat', 'INFO', or 'contig'.
vcfc:headerValue header value Domain: vcfc:HeaderLine | Range: xsd:string The source value to the right of '=' in a VCF meta-information line. For a structured line, this may preserve the angle-bracketed key-value list in addition to its separately represented attributes.
vcfc:identifierValue identifier value Domain: vcfc:RecordIdentifier | Range: xsd:string -
vcfc:infoRaw INFO raw Domain: vcfc:VariantCall | Range: rdfs:Literal An optional lossless copy of the INFO fixed-field string. In VCF it is '.' when no annotations are present, or a semicolon-separated series of key[=value[,value...]] entries. Use structured vcfc:InfoFieldValue resources for machine interpretation.
vcfc:insertedSequence inserted sequence Domain: vcfc:Breakend | Range: xsd:string -
vcfc:isImprecise is imprecise Domain: vcfc:AltAllele | Range: xsd:boolean -
vcfc:isNoCall is no-call Domain: vcfc:GenotypeAlleleCall | Range: xsd:boolean -
vcfc:isNovel is novel Domain: vcfc:AltAllele | Range: xsd:boolean -
vcfc:isReferenceBlockStart is reference-block start Domain: vcfc:ReferenceBlock | Range: xsd:boolean -
vcfc:isSingleBreakend is single breakend Domain: vcfc:Breakend | Range: xsd:boolean -
vcfc:isTelomereBreakend is telomere breakend Domain: vcfc:Breakend | Range: xsd:boolean -
vcfc:itemValue item value Domain: vcfc:FieldValueItem | Range: rdfs:Literal -
vcfc:lineIndex line index Domain: vcfc:HeaderLine | Range: xsd:positiveInteger -
vcfc:localAlleleIndex local allele index Domain: vcfc:AltAllele | Range: xsd:positiveInteger Use localIndex on LocalAlleleMembership for sample-specific ordering. alleleIndex remains the record-global ALT index written in LAA.
vcfc:localIndex local index Domain: vcfc:LocalAlleleMembership | Range: xsd:positiveInteger -
vcfc:metaAllowedValue META allowed value Domain: vcfc:MetaDefinition | Range: xsd:string -
vcfc:modificationAlleleDepth modification allele depth Domain: vcfc:BaseModification | Range: rdfs:Literal -
vcfc:modificationDepth modification depth Domain: vcfc:BaseModification | Range: rdfs:Literal -
vcfc:modificationFraction modification fraction Domain: vcfc:BaseModification | Range: rdfs:Literal -
vcfc:modifiedBaseOffset modified-base offset Domain: vcfc:BaseModification | Range: xsd:nonNegativeInteger -
vcfc:paddingAnchorPosition padding anchor position Domain: vcfc:PaddingInterpretation | Range: xsd:integer The 1-based reference coordinate of the padding base. For vcfc:PaddingBefore this equals the record's POS; for vcfc:PaddingAfter it is the coordinate following the variant bases. Absent when no padding base is asserted.
vcfc:paddingBaseCount padding base count Domain: vcfc:PaddingInterpretation | Range: xsd:nonNegativeInteger How many bases of the record's alleles serve as padding under the stated rule: one for a required padding base, zero when the rule determines that none is present or when the specification leaves it undetermined.
vcfc:pedigreeDbUrl pedigree database URL Domain: vcfc:PedigreeDBHeaderLine | Range: xsd:anyURI -
vcfc:percentEncodingPolicy percent-encoding policy Domain: vcfc:VCFFile | Range: xsd:string -
vcfc:phaseIndicator preceding phase indicator Domain: vcfc:GenotypeAlleleCall | Range: xsd:string The / or | indicator preceding this GT allele call, including the effective first indicator when omitted in the source. genotypeString preserves whether it was explicit.
vcfc:phaseSetId phase-set ID Domain: vcfc:PhaseSet | Range: xsd:string -
vcfc:phaseSetName phase-set name Domain: vcfc:PhaseSet | Range: xsd:string -
vcfc:phaseSetOrdinal phase-set ordinal Domain: vcfc:PhaseSet | Range: xsd:integer -
vcfc:phaseSetQuality phase-set quality Domain: vcfc:PhaseSet | Range: rdfs:Literal -
vcfc:ploidy ploidy Domain: vcfc:Genotype | Range: xsd:nonNegativeInteger -
vcfc:pos POS Domain: vcfc:VCFRecord | Range: xsd:integer The required 1-based reference position of the record. It denotes the first base of REF, is numerically ordered within CHROM, and may be 0 or N+1 to indicate a telomere for a contig of length N.
vcfc:qual QUAL Domain: vcfc:VariantCall | Range: rdfs:Literal The QUAL fixed-field value: the Phred-scaled quality score for the assertion made in ALT. When ALT is '.', it is -10 log10 P(variant); otherwise it is -10 log10 P(no variant). An unknown score is represented by '.'^^vcfc:Null.
vcfc:rawValue raw value Range: rdfs:Literal The lossless source lexical value before optional percent decoding.
vcfc:recordId ID Domain: vcfc:VCFRecord | Range: rdfs:Literal The ID fixed-field value: a semicolon-separated list of unique record identifiers, such as dbSNP rs identifiers. When no identifier is available, VCF uses '.', represented here as '.'^^vcfc:Null.
vcfc:recordIndex record index Domain: vcfc:VCFRecord | Range: xsd:positiveInteger -
vcfc:ref REF Domain: vcfc:VCFRecord | Range: xsd:string The required reference allele string. It contains one or more A, C, G, T, or N bases and begins at POS. For simple insertions, deletions, and symbolic alleles, VCF uses an adjacent padding base to avoid an empty allele.
vcfc:referenceBlockLength reference-block length Domain: vcfc:ReferenceBlock | Range: xsd:nonNegativeInteger -
vcfc:referenceGenome reference genome Domain: vcfc:VCFFile | Range: xsd:string The reference genome or sequence resource identified by optional reference metadata, commonly a '##reference' header value. VCF 4.5 recommends recording reference and contig metadata to make the records interpretable.
vcfc:repeatBases repeat bases Domain: vcfc:RepeatSequence | Range: rdfs:Literal -
vcfc:repeatSequenceCount repeat-sequence count Domain: vcfc:TandemRepeatAllele | Range: xsd:nonNegativeInteger -
vcfc:repeatSequenceIndex repeat-sequence index Domain: vcfc:RepeatSequence | Range: xsd:positiveInteger -
vcfc:repeatUnitBases repeat-unit bases Domain: vcfc:RepeatUnit | Range: rdfs:Literal -
vcfc:repeatUnitCount repeat-unit count Domain: vcfc:RepeatSequence | Range: rdfs:Literal -
vcfc:repeatUnitLength repeat-unit length Domain: vcfc:RepeatSequence | Range: rdfs:Literal -
vcfc:repeatUnitSequence repeat-unit sequence Domain: vcfc:RepeatSequence | Range: rdfs:Literal -
vcfc:sampleDataRaw sample data raw Domain: vcfc:CohortCallMatrix | Range: xsd:string Added in version 1.1.0. An optional lossless textual copy of a record's genotype columns, with individual sample blocks separated by tabs in SampleSet order. It preserves source serialization for a CohortCallMatrix but does not replace its FORMAT value vectors for semantic interpretation.
vcfc:sampleFieldsRaw raw sample fields Domain: vcfc:SampleCall | Range: xsd:string One expanded sample's original colon-separated fields, retaining omitted trailing fields and empty list tokens.
vcfc:sampleFilter sample filter Domain: vcfc:SampleCall | Range: rdfs:Literal The FT value on one SampleCall, preserving PASS, one or more failure codes, or the VCF missing token.
vcfc:sampleId sample ID Domain: vcfc:SampleCall | Range: xsd:string The sample identifier from the column-header line on an expanded SampleCall. When genotype data is present, VCF places FORMAT after the eight fixed columns and then one uniquely named column per sample. Since version 1.1.0, converters should additionally use vcfc:forSample and VCFSample when reusable sample identity is needed.
vcfc:sampleIndex sample index Domain: vcfc:VCFSample | Range: xsd:positiveInteger Added in version 1.1.0. The one-based position of a VCFSample in its file's '#CHROM' sample-column order. A condensed FormatValueVector position i corresponds to the SampleSet member whose sample index is i.
vcfc:sampleName sample name Domain: vcfc:VCFSample | Range: xsd:string Added in version 1.1.0. The exact sample-column identifier from the '#CHROM' header line, attached to a reusable VCFSample. It is distinct from vcfc:sampleId, which remains the identifier literal on an expanded SampleCall.
vcfc:sourceSoftware source software Domain: vcfc:VCFFile | Range: xsd:string The program, pipeline, or other source named by an optional '##source' header line.
vcfc:svClaimCode SV claim code Domain: vcfc:SVClaim | Range: xsd:string -
vcfc:svLength SV length Domain: vcfc:AltAllele | Range: rdfs:Literal -
vcfc:svTypeCode SV type code Domain: vcfc:SymbolicAlleleType | Range: xsd:string -
vcfc:tupleArity tuple arity Domain: vcfc:FieldValueItem | Range: xsd:positiveInteger The fixed grouping width for flattened VCF value lists, such as 2 for confidence intervals and 4 for MEINFO or METRANS.
vcfc:valueIndex value index Domain: vcfc:FieldValueItem | Range: xsd:nonNegativeInteger -

Annotation Properties

Declared ontology terms extracted from the configured primary source file.

Term Label Relationships Description
vcfc:aliasOf alias of No graph relationships emitted The canonical reserved key denoted by a VCF base-modification alias.
vcfc:deprecatedInVersion deprecated in version No graph relationships emitted Records the VCF specification version in which a reserved field is deprecated.
vcfc:iriTemplate IRI template No graph relationships emitted Provides a recommended IRI-minting pattern, using RFC 6570-style placeholders, for instances of a vocabulary class.
vcfc:keyPattern key pattern No graph relationships emitted The regular-expression family reserved by a FORMAT field definition rather than one concrete key.
vcfc:missingValuePolicy missing value policy No graph relationships emitted Documents how the VCF missing-value token '.' is represented when source values are transformed to RDF.
vcfc:recommendedSequenceAlterationClass recommended sequence alteration class No graph relationships emitted Documents a sequence-alteration class recommended as a target when a VCF-centric record or call is linked to a variation model. It is guidance for alignment and does not reclassify the VCF resource.
vcfc:reservedIn reserved in No graph relationships emitted Records the VCF specification version that reserves a field identifier or identifier pattern.
vcfc:specificationVersion specification version No graph relationships emitted The VCF specification version a registry graph describes. It is distinct from owl:versionInfo, which records the release version of this vocabulary.

Declared Terms

Declared ontology terms extracted from the configured primary source file.

Term Label Relationships Description
vcfc: VCF Core Vocabulary No graph relationships emitted -
vcfc:AbundanceAndAdjacencyClaim abundance and adjacency claim (DJ) No graph relationships emitted -
vcfc:AbundanceClaim abundance claim (D) No graph relationships emitted -
vcfc:AdjacencyClaim adjacency claim (J) No graph relationships emitted -
vcfc:ArityPerAllele one value per allele (R) No graph relationships emitted -
vcfc:ArityPerAlt one value per alternate allele (A) No graph relationships emitted -
vcfc:ArityPerBaseModification one value per base modification (M) No graph relationships emitted -
vcfc:ArityPerGenotype one value per genotype (G) No graph relationships emitted -
vcfc:ArityPerGTAllele one value per GT allele (P) No graph relationships emitted -
vcfc:ArityPerLocalAllele one value per local allele (LR) No graph relationships emitted -
vcfc:ArityPerLocalAlt one value per local alternate allele (LA) No graph relationships emitted -
vcfc:ArityPerLocalGenotype one value per local genotype (LG) No graph relationships emitted -
vcfc:ArityVariable variable arity (.) No graph relationships emitted -
vcfc:BaseSequenceAllele base-sequence allele No graph relationships emitted A literal base sequence in an ALT field.
vcfc:BreakendAllele breakend allele No graph relationships emitted A bracketed VCF ALT expression describing a breakend.
vcfc:BreakendString breakend string No graph relationships emitted A VCF breakend ALT lexical value. Use a Breakend resource for the queryable structural components while retaining this datatype for the lossless source expression.
vcfc:CharacterType Character No graph relationships emitted The VCF Character type, used when a field value is a single character.
vcfc:CondensedRepresentation condensed representation No graph relationships emitted Added in version 1.1.0. The representation profile that expresses a VariantCall's multi-sample genotype data through a CohortCallMatrix, a shared SampleSet, and FORMAT value vectors. It is intended for large multi-sample VCF files. Individual genotype values remain recoverable by decoding the vectors, but are not independently asserted as RDF triples.
vcfc:EventBalancedTranslocation TRA:BALANCED event type No graph relationships emitted -
vcfc:EventBreakageFusionBridge BFB event type No graph relationships emitted -
vcfc:EventChromoplexy CHROMOPLEXY event type No graph relationships emitted -
vcfc:EventChromothripsis CHROMOTHRIPSIS event type No graph relationships emitted -
vcfc:EventDeletion DEL event type No graph relationships emitted -
vcfc:EventDispersedDuplication DUP:DISPERSED event type No graph relationships emitted -
vcfc:EventDoubleMinute DOUBLEMINUTE event type No graph relationships emitted -
vcfc:EventDuplication DUP event type No graph relationships emitted -
vcfc:EventInsertion INS event type No graph relationships emitted -
vcfc:EventInversion INV event type No graph relationships emitted -
vcfc:EventMobileElementDeletion DEL:ME event type No graph relationships emitted -
vcfc:EventMobileElementInsertion INS:ME event type No graph relationships emitted -
vcfc:EventTandemDuplication DUP:TANDEM event type No graph relationships emitted -
vcfc:EventTranslocation TRA event type No graph relationships emitted -
vcfc:EventUnbalancedTranslocation TRA:UNBALANCED event type No graph relationships emitted -
vcfc:ExpandedRepresentation expanded representation No graph relationships emitted Added in version 1.1.0 as vcfr:DenseRepresentation and renamed in version 2.0.0 to match the terminology used throughout the documentation. The representation profile that expresses genotype data as a vcfc:SampleCall for each sample and a vcfc:FormatFieldValue for each populated sample/FORMAT position. It is intended for single-sample or low-sample VCF files and for use cases requiring direct RDF statements about individual calls.
vcfc:FiltersFailed filters failed No graph relationships emitted -
vcfc:FiltersNotApplied filters not applied No graph relationships emitted -
vcfc:FiltersPassed filters passed No graph relationships emitted -
vcfc:FlagType Flag No graph relationships emitted The VCF presence-only type for an INFO key. A Flag has no value in the INFO column and its Number is 0; it is not permitted for FORMAT fields.
vcfc:FloatType Float No graph relationships emitted The VCF Float type: a 32-bit IEEE-754 floating-point value, whose textual form may also express INF, INFINITY, or NAN.
vcfc:GenotypeString genotype string No graph relationships emitted A VCF GT lexical value: allele indices or missing calls separated by phased (|) or unphased (/) indicators, optionally with a leading indicator for partial phasing.
vcfc:IntegerType Integer No graph relationships emitted The VCF Integer type: a signed 32-bit integer value.
vcfc:MissingAllele missing allele (.) No graph relationships emitted The VCF missing ALT token.
vcfc:MixedPhasing mixed phasing No graph relationships emitted Both phased and unphased allele indicators occur; phaseIndicator on each allele call supplies the precise semantics.
vcfc:Null null literal datatype No graph relationships emitted Datatype for the explicit VCF missing-value token '.'. VCF 4.5 uses this token whenever a field or allele value is missing; represent it as '.'^^vcfc:Null rather than as a plain string or a fabricated numeric value.
vcfc:OverlappingDeletionAllele overlapping-deletion allele (*) No graph relationships emitted The star ALT allele, marking an allele deleted by an overlapping upstream record.
vcfc:PaddingAfter padding after the variant No graph relationships emitted The position-one exception: the padding base follows the variant bases.
vcfc:PaddingBefore padding before the variant No graph relationships emitted The ordinary case: the padding base is the first base of REF and POS denotes it.
vcfc:PaddingNotDetermined not determined by the specification No graph relationships emitted Every allele already has at least one base of its own, so VCF 4.5 permits but does not require a padding base and does not say which base plays that role. No padding claim is made; the shared prefix of a complex substitution falls here.
vcfc:Phased phased No graph relationships emitted -
vcfc:PositionOnePadding contig position one exception No graph relationships emitted The variant occurs at position 1 of the contig, where VCF 4.5 requires the base after the variant instead of the base before it.
vcfc:ReservedFormat_AD Format AD reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADF Format ADF reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADM5caC Format ADM5caC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADM5caU Format ADM5caU reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADM5fC Format ADM5fC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADM5fU Format ADM5fU reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADM5hmC Format ADM5hmC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADM5hmU Format ADM5hmU reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADM5mC Format ADM5mC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADM6mA Format ADM6mA reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADM8oxoG Format ADM8oxoG reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADMChEBI_ACGTUN_ Format ADM[0-9]+[ACGTUN] reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADMXaoN Format ADMXaoN reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_ADR Format ADR reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_AHAP Format AHAP reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_CICN Format CICN reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_CN Format CN reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_CNL Format CNL reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_CNP Format CNP reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_CNQ Format CNQ reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_DP Format DP reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_DPM5caC Format DPM5caC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_DPM5caU Format DPM5caU reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_DPM5fC Format DPM5fC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_DPM5fU Format DPM5fU reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_DPM5hmC Format DPM5hmC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_DPM5hmU Format DPM5hmU reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_DPM5mC Format DPM5mC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_DPM6mA Format DPM6mA reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_DPM8oxoG Format DPM8oxoG reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_DPMChEBI_ACGTUN_ Format DPM[0-9]+[ACGTUN] reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_DPMXaoN Format DPMXaoN reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_EC Format EC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_FT Format FT reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_GL Format GL reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_GP Format GP reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_GQ Format GQ reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_GT Format GT reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_HAP Format HAP reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_HQ Format HQ reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_LA Format LA reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_LAA Format LAA reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_LAD Format LAD reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_LADF Format LADF reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_LADR Format LADR reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_LEC Format LEC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_LEN Format LEN reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_LGL Format LGL reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_LGP Format LGP reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_LPL Format LPL reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_LPP Format LPP reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_M5caC Format M5caC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_M5caU Format M5caU reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_M5fC Format M5fC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_M5fU Format M5fU reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_M5hmC Format M5hmC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_M5hmU Format M5hmU reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_M5mC Format M5mC reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_M6mA Format M6mA reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_M8oxoG Format M8oxoG reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_MChEBI_ACGTUN_ Format M[0-9]+[ACGTUN] reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_MQ Format MQ reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_MXaoN Format MXaoN reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_NQ Format NQ reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_PL Format PL reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_PP Format PP reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_PQ Format PQ reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_PS Format PS reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_PSL Format PSL reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_PSO Format PSO reserved field definition No graph relationships emitted -
vcfc:ReservedFormat_PSQ Format PSQ reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_1000G Info 1000G reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_AA Info AA reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_AC Info AC reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_AD Info AD reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_ADF Info ADF reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_ADR Info ADR reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_AF Info AF reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_AN Info AN reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_BKPTID Info BKPTID reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_BQ Info BQ reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_CICN Info CICN reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_CIEND Info CIEND reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_CIGAR Info CIGAR reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_CILEN Info CILEN reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_CIPOS Info CIPOS reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_CIRB Info CIRB reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_CIRUC Info CIRUC reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_CN Info CN reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_DB Info DB reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_DBRIPID Info DBRIPID reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_DBVARID Info DBVARID reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_DGVID Info DGVID reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_DP Info DP reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_END Info END reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_EVENT Info EVENT reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_EVENTTYPE Info EVENTTYPE reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_H2 Info H2 reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_H3 Info H3 reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_HOMLEN Info HOMLEN reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_HOMSEQ Info HOMSEQ reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_IMPRECISE Info IMPRECISE reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_MATEID Info MATEID reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_MEINFO Info MEINFO reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_METRANS Info METRANS reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_MQ Info MQ reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_MQ0 Info MQ0 reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_NOVEL Info NOVEL reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_NS Info NS reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_PARID Info PARID reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_RB Info RB reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_RN Info RN reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_RUB Info RUB reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_RUC Info RUC reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_RUL Info RUL reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_RUS Info RUS reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_SB Info SB reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_SOMATIC Info SOMATIC reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_SVCLAIM Info SVCLAIM reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_SVLEN Info SVLEN reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_SVTYPE Info SVTYPE reserved field definition No graph relationships emitted -
vcfc:ReservedInfo_VALIDATED Info VALIDATED reserved field definition No graph relationships emitted -
vcfc:SequenceAfterLeftBracket sequence after left bracket No graph relationships emitted The [p[t breakend form.
vcfc:SequenceAfterRightBracket sequence after right bracket No graph relationships emitted The ]p]t breakend form.
vcfc:SequenceBeforeLeftBracket sequence before left bracket No graph relationships emitted The t[p[ breakend form.
vcfc:SequenceBeforeRightBracket sequence before right bracket No graph relationships emitted The t]p] breakend form.
vcfc:SimpleIndelPadding simple insertion or deletion No graph relationships emitted One allele is a strict prefix of the other, so without a padding base one allele would be empty. VCF 4.5 requires the base before the variant, and POS denotes that base.
vcfc:StringType String No graph relationships emitted The VCF String type, used for a textual value whose permitted content is further constrained by the field in which it occurs.
vcfc:SymbolicAllele symbolic allele No graph relationships emitted An angle-bracketed symbolic ALT identifier such as <DEL>.
vcfc:SymbolicAllelePadding symbolic alternate allele No graph relationships emitted An ALT allele is an angle-bracketed symbolic ID other than '<*>'. VCF 4.5 requires the padding base and POS denotes the coordinate of the base preceding the polymorphism.
vcfc:SymbolicCopyNumberVariation CNV symbolic allele type No graph relationships emitted -
vcfc:SymbolicDeletion DEL symbolic allele type No graph relationships emitted -
vcfc:SymbolicDuplication DUP symbolic allele type No graph relationships emitted -
vcfc:SymbolicInsertion INS symbolic allele type No graph relationships emitted -
vcfc:SymbolicInversion INV symbolic allele type No graph relationships emitted -
vcfc:SymbolicMobileElementDeletion DEL:ME symbolic allele subtype No graph relationships emitted -
vcfc:SymbolicMobileElementInsertion INS:ME symbolic allele subtype No graph relationships emitted -
vcfc:SymbolicTandemDuplication DUP:TANDEM symbolic allele subtype No graph relationships emitted -
vcfc:SymbolicTandemRepeat CNV:TR symbolic allele subtype No graph relationships emitted -
vcfc:Unphased unphased No graph relationships emitted -
vcfc:UnspecifiedAllele unspecified allele No graph relationships emitted The <*> or <NON_REF> ALT form used to indicate an unspecified alternate allele.
vcfc:UnspecifiedAlleleNoPadding unspecified allele, no padding No graph relationships emitted The only alternate allele is the unspecified allele '<*>', which VCF 4.5 exempts from the padding requirement: its reference call interval includes the POS base. The padding base count is therefore zero.
vcfc:VCFFloat VCF Float No graph relationships emitted A VCF Float lexical value: a finite decimal/scientific value or, case-insensitively, INF, INFINITY, or NAN. SHACL supplies the portable lexical check.
vcfc:VCFInteger VCF Integer No graph relationships emitted A signed 32-bit VCF Integer excluding -2147483648 through -2147483641, which VCF 4.5 reserves because BCF cannot encode them.
vcfc:VCFTextVector VCF text vector encoding No graph relationships emitted Added in version 1.1.0. A tab-separated sequence of raw VCF values, ordered by the matrix SampleSet. There is exactly one item per sample; a missing item is represented by the VCF token '.'. Commas within an item remain part of that FORMAT value and MUST NOT be treated as vector separators.