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Term Pages

Every declared ontology term gets its own generated HTML page when features.termPages is enabled.

Classes

78 declared classes in the configured ontology.

Term Type Label Description
vcfc:Allele Class VCF allele 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 Class VCF allele kind A controlled syntactic category for an allele lexical form.
vcfc:AltAllele Class alternate allele One ordered ALT allele, identified by a positive alleleIndex in source ALT order.
vcfc:AltDefinition Class ALT definition 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 Class ALT header line 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 Class breakpoint-assembly contig 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 Class assembly header line The optional ##assembly line that locates a FASTA file containing breakpoint assemblies referenced by BKPTID.
vcfc:BaseModification Class base modification 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 Class breakend A parsed bracketed VCF ALT allele representing a novel adjacency or terminus. The source expression remains in alleleValue.
vcfc:BreakendOrientation Class breakend orientation One of the four bracket placements permitted by VCF breakend notation.
vcfc:CohortCallMatrix Class cohort call matrix 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 Class column header line 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 Class confidence interval 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 Class contig header line 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 Class event type A reserved VCF EVENTTYPE code.
vcfc:FieldDefinition Class field definition 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 Class field value item 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 Class fileDate header line 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 Class fileformat header line The required, first VCF meta-information line. Its value declares the VCF version, for example 'VCFv4.5'.
vcfc:FilterCode Class filter failure code One failed FILTER or FT code. PASS and missing are statuses, not failure codes.
vcfc:FilterDefinition Class FILTER definition 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 Class FILTER header line 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 Class filter status -
vcfc:FormatFieldDefinition Class FORMAT field definition 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 Class FORMAT field value 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 Class FORMAT header line 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 Class declared FORMAT key 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 Class FORMAT value vector 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 Class VCF genotype The parsed GT field for one SampleCall. It preserves genotypeString and represents its ordered allele calls and phasing independently.
vcfc:GenotypeAlleleCall Class genotype allele call One allele position in a parsed GT value. callIndex preserves genotype order; isNoCall represents a dot call without inventing an allele.
vcfc:HeaderAttribute Class header attribute 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 Class VCF header line 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 Class INFO field definition 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 Class INFO field value 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 Class INFO header line 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 Class local allele membership An ordered membership in one sample's LocalAlleleSet. The membership, rather than the shared ALT allele, carries the local index.
vcfc:LocalAlleleSet Class local allele set The subset of ALT alleles declared as locally relevant to a sample by LAA. Its members keep their record-global alleleIndex values.
vcfc:MetaDefinition Class META definition A ##META declaration represented as a reusable field definition. Its fieldId, fieldArity, and fieldType describe attributes used on ##SAMPLE lines.
vcfc:MetaHeaderLine Class META header line A structured ##META declaration that defines an implementation- or file-specific sample attribute key and optional allowed values.
vcfc:PaddingInterpretation Class padding-base interpretation 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 Class padding rule 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 Class padding side Whether the padding base precedes or follows the variant bases.
vcfc:PedigreeDBHeaderLine Class pedigreeDB header line The optional ##pedigreeDB line that identifies an external pedigree database.
vcfc:PedigreeHeaderLine Class PEDIGREE header line 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 Class pedigree relation A parent, ancestor, or clonal-origin relationship declared in VCF pedigree metadata.
vcfc:PhaseSet Class phase set A parsed phase-set identifier or list carried by PS or PSL, optionally with PSO and PSQ information.
vcfc:PhasingStatus Class phasing status The separator semantics between genotype allele calls.
vcfc:RecordIdentifier Class record identifier One component of the semicolon-separated ID column. The missing dot is represented by no identifier components.
vcfc:ReferenceAllele Class reference allele The record's REF allele, identified by alleleIndex 0.
vcfc:ReferenceBlock Class reference block 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 Class reference header line 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 Class repeat sequence One repeat sequence within a tandem-repeat allele, indexed in VCF RN/RUS/RUL/RUC/RB order.
vcfc:RepeatUnit Class repeat unit One individually sized repeat unit used only when RUB distinguishes varying unit lengths.
vcfc:RepresentationProfile Class VCF RDF representation profile 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 Class sample call 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 Class sample declaration 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 Class SAMPLE header line A structured ##SAMPLE declaration describing a sample or genome mapping through standard or META-declared attributes.
vcfc:SampleSet Class VCF sample set 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 Class source header line An optional producer-supplied '##source' meta-information line, typically identifying the program, pipeline, or source that generated the VCF.
vcfc:StructuredHeaderLine Class structured header line 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 Class structural-variant claim The per-ALT SVCLAIM code indicating an abundance claim, adjacency claim, or both.
vcfc:SymbolicAlleleType Class symbolic allele type 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 Class tandem-repeat allele A <CNV:TR> alternate allele whose repeat sequences and units are represented through the VCF tandem-repeat fields.
vcfc:UnstructuredHeaderLine Class unstructured header line A VCF meta-information line whose non-empty value is not an angle-bracketed attribute list.
vcfc:VariantCall Class variant call 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 Class variant event A named EVENT grouping records that jointly describe a complex rearrangement or another related variation event.
vcfc:VCF41File Class VCF 4.1 file 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 Class VCF 4.2 file 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 Class VCF 4.3 file 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 Class VCF 4.4 file 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 Class VCF 4.5 file 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 Class VCF file 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 Class VCF header 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 Class VCF Number arity 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 Class VCF record 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 Class VCF sample 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 Class VCF value type 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 Class FORMAT value vector encoding 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

75 declared object properties in the configured ontology.

Term Type Label Description
vcfc:alleleKind Object Property allele kind -
vcfc:allelePhaseSet Object Property allele phase set The PSL entry for this GT allele call; missing entries have no link.
vcfc:appliesToSampleSet Object Property applies to sample set Added in version 1.1.0. Identifies the ordered SampleSet used to interpret a CohortCallMatrix and all of its FORMAT value vectors.
vcfc:asSequenceAlteration Object Property as sequence alteration 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 Object Property block allele -
vcfc:breakendOrientation Object Property breakend orientation -
vcfc:calledAllele Object Property called allele -
vcfc:chromAssemblyContig Object Property CHROM assembly contig 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 Object Property chromosome / contig reference 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 Object Property copy-number confidence interval -
vcfc:declaredBy Object Property declared by 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 Object Property declared by ALT definition -
vcfc:declaredByFilter Object Property declared by filter -
vcfc:declaredInAssembly Object Property declared in assembly file 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 Object Property declared on header line 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 Object Property declares sample -
vcfc:endConfidenceInterval Object Property END confidence interval Represents CIEND through FALDO InRangePosition rather than a VCF-specific ConfidenceInterval.
vcfc:eventType Object Property event type -
vcfc:fieldArity Object Property field arity 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 Object Property field Type 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 Object Property filter status Status of FILTER on a VariantCall or FT on a SampleCall.
vcfc:forAllele Object Property for allele -
vcfc:forBaseModification Object Property for base modification Links a Number=M value item to the applicable BaseModification resource when that layer is used.
vcfc:forSample Object Property for sample 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 Object Property has allele call -
vcfc:hasAltAllele Object Property has alternate allele -
vcfc:hasAttribute Object Property has attribute -
vcfc:hasCall Object Property has call Associates a VCF record with its vocabulary-level call resource, which groups QUAL, FILTER, INFO, FORMAT, and per-sample call data.
vcfc:hasCallMatrix Object Property has cohort call matrix 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 Object Property has column header -
vcfc:hasFilterCode Object Property has filter failure code -
vcfc:hasFormatKey Object Property has declared FORMAT key 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 Object Property has FORMAT value Associates a sample call with one structured value parsed from that sample's FORMAT-ordered data block.
vcfc:hasFormatValueVector Object Property has FORMAT value vector Added in version 1.1.0. Associates a CohortCallMatrix with the ordered values for one FORMAT key across its SampleSet.
vcfc:hasGenotype Object Property has genotype -
vcfc:hasGenotypeColumns Object Property has genotype columns -
vcfc:hasHeader Object Property has header Associates a VCF file artifact with the resource that groups its meta-information header lines.
vcfc:hasHeaderLine Object Property has header line 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 Object Property has identifier -
vcfc:hasInfoValue Object Property has INFO value Associates a record-level call with one structured annotation parsed from its INFO column.
vcfc:hasLocalAllele Object Property has local allele -
vcfc:hasLocalAlleleMembership Object Property has local allele membership -
vcfc:hasLocalAlleleSet Object Property has local allele set -
vcfc:hasPaddingInterpretation Object Property has padding interpretation Associates a record with the padding interpretation derived for its alleles. At most one interpretation is asserted per record.
vcfc:hasRecord Object Property has record Associates a VCF file with one of its tab-delimited data records.
vcfc:hasReferenceAllele Object Property has reference allele -
vcfc:hasReferenceBlock Object Property has reference block -
vcfc:hasRepeatSequence Object Property has repeat sequence -
vcfc:hasRepeatUnit Object Property has repeat unit -
vcfc:hasSample Object Property has sample 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 Object Property has sample call 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 Object Property has sample set 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 Object Property has value item -
vcfc:inEvent Object Property in event -
vcfc:inPhaseSet Object Property in phase set -
vcfc:lenConfidenceInterval Object Property SVLEN confidence interval -
vcfc:localAllele Object Property local allele -
vcfc:mateBreakend Object Property mate breakend -
vcfc:modifiedResidue Object Property modified residue Links directly to the ChEBI class denoting the modified residue.
vcfc:paddingRule Object Property padding rule The specification provision that produced this padding interpretation.
vcfc:paddingSide Object Property padding side Which side of the variant bases the padding base occupies. Asserted only when a padding rule determines it.
vcfc:partnerBreakend Object Property partner breakend -
vcfc:pedigreeAncestor Object Property pedigree ancestor -
vcfc:pedigreeFather Object Property pedigree father -
vcfc:pedigreeMother Object Property pedigree mother -
vcfc:pedigreeOriginal Object Property pedigree original 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 Object Property phasing status -
vcfc:posConfidenceInterval Object Property POS confidence interval Represents CIPOS through FALDO InRangePosition rather than a VCF-specific ConfidenceInterval.
vcfc:rbConfidenceInterval Object Property RB confidence interval -
vcfc:representationProfile Object Property representation profile 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 Object Property RUC confidence interval -
vcfc:svClaim Object Property SV claim -
vcfc:svSubtypeOf Object Property SV subtype of -
vcfc:svType Object Property SV type -
vcfc:valueEncoding Object Property value encoding Added in version 1.1.0. Names the lexical encoding used for a FormatValueVector's vcfc:encodedValues payload.

Datatype Properties

111 declared datatype properties in the configured ontology.

Term Type Label Description
vcfc:alleleIndex Datatype Property allele index -
vcfc:alleleValue Datatype Property allele value -
vcfc:alt Datatype Property ALT 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 Datatype Property ALT ID The ID of a symbolic ALT declaration, stored without the angle brackets used when the identifier occurs in the ALT column.
vcfc:ancestorRole Datatype Property ancestor role -
vcfc:ancestralHaplotypeId Datatype Property ancestral haplotype ID -
vcfc:arityCode Datatype Property arity code -
vcfc:assemblyContigId Datatype Property assembly contig ID 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 Datatype Property assembly URL -
vcfc:attributeIndex Datatype Property attribute index -
vcfc:attributeKey Datatype Property attribute key -
vcfc:attributeValue Datatype Property attribute value -
vcfc:breakendReplacementString Datatype Property breakend replacement string -
vcfc:callIndex Datatype Property allele-call index -
vcfc:chrom Datatype Property CHROM 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 Datatype Property confidence-interval lower bound -
vcfc:ciUpper Datatype Property confidence-interval upper bound -
vcfc:componentIndex Datatype Property component index One-based position of an ID or FILTER component in its source column.
vcfc:contigAssembly Datatype Property contig assembly An optional assembly identifier supplied in a contig declaration. It identifies the reference assembly context for the named contig.
vcfc:contigCount Datatype Property contig count The number of contig declarations associated with the file. This is a derived RDF convenience, not a separate VCF header field.
vcfc:contigId Datatype Property contig ID 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 Datatype Property contig length The optional 'length' attribute of a contig declaration: the length of the reference sequence in bases.
vcfc:contigMd5 Datatype Property contig MD5 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 Datatype Property contig URL -
vcfc:copyNumber Datatype Property copy number -
vcfc:copyNumberLikelihood Datatype Property copy-number likelihood -
vcfc:copyNumberPosterior Datatype Property copy-number posterior -
vcfc:copyNumberQuality Datatype Property copy-number quality -
vcfc:decodedValue Datatype Property decoded value A consumer-oriented value after applying the file's percent-encoding policy; rawValue remains authoritative for round-tripping.
vcfc:encodedValues Datatype Property encoded values 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 Datatype Property end position -
vcfc:eventTypeCode Datatype Property event type code -
vcfc:fieldDescription Datatype Property field Description 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 Datatype Property field ID 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 Datatype Property field index One-based source order of an INFO entry or FORMAT field value within its parent.
vcfc:fieldNumber Datatype Property field Number 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 Datatype Property field Number integer -
vcfc:fieldSource Datatype Property field source -
vcfc:fieldValue Datatype Property field value 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 Datatype Property field value (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 Datatype Property field value (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 Datatype Property field value (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 Datatype Property field version -
vcfc:fileDate Datatype Property file 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 Datatype Property file format 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 Datatype Property FILTER 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 Datatype Property filter code value -
vcfc:filterId Datatype Property FILTER ID 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 Datatype Property for genotype index -
vcfc:forGTAlleleIndex Datatype Property for GT allele index -
vcfc:formatRaw Datatype Property FORMAT raw 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 Datatype Property genotype index The VCF Number=G index for genotype alleles k₁…k_P: Index(k₁…k_P) = Σ C(k_m + m − 1, m).
vcfc:genotypeString Datatype Property genotype string -
vcfc:haplotypeId Datatype Property haplotype ID -
vcfc:headerKey Datatype Property header key The meta-information key to the left of '=' in a header line, without the leading '##'; for example, 'fileformat', 'INFO', or 'contig'.
vcfc:headerValue Datatype Property header value 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 Datatype Property identifier value -
vcfc:infoRaw Datatype Property INFO raw 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 Datatype Property inserted sequence -
vcfc:isImprecise Datatype Property is imprecise -
vcfc:isNoCall Datatype Property is no-call -
vcfc:isNovel Datatype Property is novel -
vcfc:isReferenceBlockStart Datatype Property is reference-block start -
vcfc:isSingleBreakend Datatype Property is single breakend -
vcfc:isTelomereBreakend Datatype Property is telomere breakend -
vcfc:itemValue Datatype Property item value -
vcfc:lineIndex Datatype Property line index -
vcfc:localAlleleIndex Datatype Property local allele index Use localIndex on LocalAlleleMembership for sample-specific ordering. alleleIndex remains the record-global ALT index written in LAA.
vcfc:localIndex Datatype Property local index -
vcfc:metaAllowedValue Datatype Property META allowed value -
vcfc:modificationAlleleDepth Datatype Property modification allele depth -
vcfc:modificationDepth Datatype Property modification depth -
vcfc:modificationFraction Datatype Property modification fraction -
vcfc:modifiedBaseOffset Datatype Property modified-base offset -
vcfc:paddingAnchorPosition Datatype Property padding anchor position 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 Datatype Property padding base count 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 Datatype Property pedigree database URL -
vcfc:percentEncodingPolicy Datatype Property percent-encoding policy -
vcfc:phaseIndicator Datatype Property preceding phase indicator 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 Datatype Property phase-set ID -
vcfc:phaseSetName Datatype Property phase-set name -
vcfc:phaseSetOrdinal Datatype Property phase-set ordinal -
vcfc:phaseSetQuality Datatype Property phase-set quality -
vcfc:ploidy Datatype Property ploidy -
vcfc:pos Datatype Property POS 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 Datatype Property QUAL 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 Datatype Property raw value The lossless source lexical value before optional percent decoding.
vcfc:recordId Datatype Property ID 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 Datatype Property record index -
vcfc:ref Datatype Property REF 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 Datatype Property reference-block length -
vcfc:referenceGenome Datatype Property reference genome 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 Datatype Property repeat bases -
vcfc:repeatSequenceCount Datatype Property repeat-sequence count -
vcfc:repeatSequenceIndex Datatype Property repeat-sequence index -
vcfc:repeatUnitBases Datatype Property repeat-unit bases -
vcfc:repeatUnitCount Datatype Property repeat-unit count -
vcfc:repeatUnitLength Datatype Property repeat-unit length -
vcfc:repeatUnitSequence Datatype Property repeat-unit sequence -
vcfc:sampleDataRaw Datatype Property sample data raw 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 Datatype Property raw sample fields One expanded sample's original colon-separated fields, retaining omitted trailing fields and empty list tokens.
vcfc:sampleFilter Datatype Property sample filter The FT value on one SampleCall, preserving PASS, one or more failure codes, or the VCF missing token.
vcfc:sampleId Datatype Property sample ID 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 Datatype Property sample index 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 Datatype Property sample name 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 Datatype Property source software The program, pipeline, or other source named by an optional '##source' header line.
vcfc:svClaimCode Datatype Property SV claim code -
vcfc:svLength Datatype Property SV length -
vcfc:svTypeCode Datatype Property SV type code -
vcfc:tupleArity Datatype Property tuple arity The fixed grouping width for flattened VCF value lists, such as 2 for confidence intervals and 4 for MEINFO or METRANS.
vcfc:valueIndex Datatype Property value index -

Annotation Properties

8 declared annotation properties in the configured ontology.

Term Type Label Description
vcfc:aliasOf Annotation Property alias of The canonical reserved key denoted by a VCF base-modification alias.
vcfc:deprecatedInVersion Annotation Property deprecated in version Records the VCF specification version in which a reserved field is deprecated.
vcfc:iriTemplate Annotation Property IRI template Provides a recommended IRI-minting pattern, using RFC 6570-style placeholders, for instances of a vocabulary class.
vcfc:keyPattern Annotation Property key pattern The regular-expression family reserved by a FORMAT field definition rather than one concrete key.
vcfc:missingValuePolicy Annotation Property missing value policy Documents how the VCF missing-value token '.' is represented when source values are transformed to RDF.
vcfc:recommendedSequenceAlterationClass Annotation Property recommended sequence alteration class 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 Annotation Property reserved in Records the VCF specification version that reserves a field identifier or identifier pattern.
vcfc:specificationVersion Annotation Property specification version The VCF specification version a registry graph describes. It is distinct from owl:versionInfo, which records the release version of this vocabulary.

Declared Terms

195 declared declared terms in the configured ontology.

Term Type Label Description
vcfc: Declared Term VCF Core Vocabulary -
vcfc:AbundanceAndAdjacencyClaim Declared Term abundance and adjacency claim (DJ) -
vcfc:AbundanceClaim Declared Term abundance claim (D) -
vcfc:AdjacencyClaim Declared Term adjacency claim (J) -
vcfc:ArityPerAllele Declared Term one value per allele (R) -
vcfc:ArityPerAlt Declared Term one value per alternate allele (A) -
vcfc:ArityPerBaseModification Declared Term one value per base modification (M) -
vcfc:ArityPerGenotype Declared Term one value per genotype (G) -
vcfc:ArityPerGTAllele Declared Term one value per GT allele (P) -
vcfc:ArityPerLocalAllele Declared Term one value per local allele (LR) -
vcfc:ArityPerLocalAlt Declared Term one value per local alternate allele (LA) -
vcfc:ArityPerLocalGenotype Declared Term one value per local genotype (LG) -
vcfc:ArityVariable Declared Term variable arity (.) -
vcfc:BaseSequenceAllele Declared Term base-sequence allele A literal base sequence in an ALT field.
vcfc:BreakendAllele Declared Term breakend allele A bracketed VCF ALT expression describing a breakend.
vcfc:BreakendString Declared Term breakend string 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 Declared Term Character The VCF Character type, used when a field value is a single character.
vcfc:CondensedRepresentation Declared Term condensed representation 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 Declared Term TRA:BALANCED event type -
vcfc:EventBreakageFusionBridge Declared Term BFB event type -
vcfc:EventChromoplexy Declared Term CHROMOPLEXY event type -
vcfc:EventChromothripsis Declared Term CHROMOTHRIPSIS event type -
vcfc:EventDeletion Declared Term DEL event type -
vcfc:EventDispersedDuplication Declared Term DUP:DISPERSED event type -
vcfc:EventDoubleMinute Declared Term DOUBLEMINUTE event type -
vcfc:EventDuplication Declared Term DUP event type -
vcfc:EventInsertion Declared Term INS event type -
vcfc:EventInversion Declared Term INV event type -
vcfc:EventMobileElementDeletion Declared Term DEL:ME event type -
vcfc:EventMobileElementInsertion Declared Term INS:ME event type -
vcfc:EventTandemDuplication Declared Term DUP:TANDEM event type -
vcfc:EventTranslocation Declared Term TRA event type -
vcfc:EventUnbalancedTranslocation Declared Term TRA:UNBALANCED event type -
vcfc:ExpandedRepresentation Declared Term expanded representation 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 Declared Term filters failed -
vcfc:FiltersNotApplied Declared Term filters not applied -
vcfc:FiltersPassed Declared Term filters passed -
vcfc:FlagType Declared Term Flag 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 Declared Term Float The VCF Float type: a 32-bit IEEE-754 floating-point value, whose textual form may also express INF, INFINITY, or NAN.
vcfc:GenotypeString Declared Term genotype string 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 Declared Term Integer The VCF Integer type: a signed 32-bit integer value.
vcfc:MissingAllele Declared Term missing allele (.) The VCF missing ALT token.
vcfc:MixedPhasing Declared Term mixed phasing Both phased and unphased allele indicators occur; phaseIndicator on each allele call supplies the precise semantics.
vcfc:Null Declared Term null literal datatype 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 Declared Term overlapping-deletion allele (*) The star ALT allele, marking an allele deleted by an overlapping upstream record.
vcfc:PaddingAfter Declared Term padding after the variant The position-one exception: the padding base follows the variant bases.
vcfc:PaddingBefore Declared Term padding before the variant The ordinary case: the padding base is the first base of REF and POS denotes it.
vcfc:PaddingNotDetermined Declared Term not determined by the specification 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 Declared Term phased -
vcfc:PositionOnePadding Declared Term contig position one exception 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 Declared Term Format AD reserved field definition -
vcfc:ReservedFormat_ADF Declared Term Format ADF reserved field definition -
vcfc:ReservedFormat_ADM5caC Declared Term Format ADM5caC reserved field definition -
vcfc:ReservedFormat_ADM5caU Declared Term Format ADM5caU reserved field definition -
vcfc:ReservedFormat_ADM5fC Declared Term Format ADM5fC reserved field definition -
vcfc:ReservedFormat_ADM5fU Declared Term Format ADM5fU reserved field definition -
vcfc:ReservedFormat_ADM5hmC Declared Term Format ADM5hmC reserved field definition -
vcfc:ReservedFormat_ADM5hmU Declared Term Format ADM5hmU reserved field definition -
vcfc:ReservedFormat_ADM5mC Declared Term Format ADM5mC reserved field definition -
vcfc:ReservedFormat_ADM6mA Declared Term Format ADM6mA reserved field definition -
vcfc:ReservedFormat_ADM8oxoG Declared Term Format ADM8oxoG reserved field definition -
vcfc:ReservedFormat_ADMChEBI_ACGTUN_ Declared Term Format ADM[0-9]+[ACGTUN] reserved field definition -
vcfc:ReservedFormat_ADMXaoN Declared Term Format ADMXaoN reserved field definition -
vcfc:ReservedFormat_ADR Declared Term Format ADR reserved field definition -
vcfc:ReservedFormat_AHAP Declared Term Format AHAP reserved field definition -
vcfc:ReservedFormat_CICN Declared Term Format CICN reserved field definition -
vcfc:ReservedFormat_CN Declared Term Format CN reserved field definition -
vcfc:ReservedFormat_CNL Declared Term Format CNL reserved field definition -
vcfc:ReservedFormat_CNP Declared Term Format CNP reserved field definition -
vcfc:ReservedFormat_CNQ Declared Term Format CNQ reserved field definition -
vcfc:ReservedFormat_DP Declared Term Format DP reserved field definition -
vcfc:ReservedFormat_DPM5caC Declared Term Format DPM5caC reserved field definition -
vcfc:ReservedFormat_DPM5caU Declared Term Format DPM5caU reserved field definition -
vcfc:ReservedFormat_DPM5fC Declared Term Format DPM5fC reserved field definition -
vcfc:ReservedFormat_DPM5fU Declared Term Format DPM5fU reserved field definition -
vcfc:ReservedFormat_DPM5hmC Declared Term Format DPM5hmC reserved field definition -
vcfc:ReservedFormat_DPM5hmU Declared Term Format DPM5hmU reserved field definition -
vcfc:ReservedFormat_DPM5mC Declared Term Format DPM5mC reserved field definition -
vcfc:ReservedFormat_DPM6mA Declared Term Format DPM6mA reserved field definition -
vcfc:ReservedFormat_DPM8oxoG Declared Term Format DPM8oxoG reserved field definition -
vcfc:ReservedFormat_DPMChEBI_ACGTUN_ Declared Term Format DPM[0-9]+[ACGTUN] reserved field definition -
vcfc:ReservedFormat_DPMXaoN Declared Term Format DPMXaoN reserved field definition -
vcfc:ReservedFormat_EC Declared Term Format EC reserved field definition -
vcfc:ReservedFormat_FT Declared Term Format FT reserved field definition -
vcfc:ReservedFormat_GL Declared Term Format GL reserved field definition -
vcfc:ReservedFormat_GP Declared Term Format GP reserved field definition -
vcfc:ReservedFormat_GQ Declared Term Format GQ reserved field definition -
vcfc:ReservedFormat_GT Declared Term Format GT reserved field definition -
vcfc:ReservedFormat_HAP Declared Term Format HAP reserved field definition -
vcfc:ReservedFormat_HQ Declared Term Format HQ reserved field definition -
vcfc:ReservedFormat_LA Declared Term Format LA reserved field definition -
vcfc:ReservedFormat_LAA Declared Term Format LAA reserved field definition -
vcfc:ReservedFormat_LAD Declared Term Format LAD reserved field definition -
vcfc:ReservedFormat_LADF Declared Term Format LADF reserved field definition -
vcfc:ReservedFormat_LADR Declared Term Format LADR reserved field definition -
vcfc:ReservedFormat_LEC Declared Term Format LEC reserved field definition -
vcfc:ReservedFormat_LEN Declared Term Format LEN reserved field definition -
vcfc:ReservedFormat_LGL Declared Term Format LGL reserved field definition -
vcfc:ReservedFormat_LGP Declared Term Format LGP reserved field definition -
vcfc:ReservedFormat_LPL Declared Term Format LPL reserved field definition -
vcfc:ReservedFormat_LPP Declared Term Format LPP reserved field definition -
vcfc:ReservedFormat_M5caC Declared Term Format M5caC reserved field definition -
vcfc:ReservedFormat_M5caU Declared Term Format M5caU reserved field definition -
vcfc:ReservedFormat_M5fC Declared Term Format M5fC reserved field definition -
vcfc:ReservedFormat_M5fU Declared Term Format M5fU reserved field definition -
vcfc:ReservedFormat_M5hmC Declared Term Format M5hmC reserved field definition -
vcfc:ReservedFormat_M5hmU Declared Term Format M5hmU reserved field definition -
vcfc:ReservedFormat_M5mC Declared Term Format M5mC reserved field definition -
vcfc:ReservedFormat_M6mA Declared Term Format M6mA reserved field definition -
vcfc:ReservedFormat_M8oxoG Declared Term Format M8oxoG reserved field definition -
vcfc:ReservedFormat_MChEBI_ACGTUN_ Declared Term Format M[0-9]+[ACGTUN] reserved field definition -
vcfc:ReservedFormat_MQ Declared Term Format MQ reserved field definition -
vcfc:ReservedFormat_MXaoN Declared Term Format MXaoN reserved field definition -
vcfc:ReservedFormat_NQ Declared Term Format NQ reserved field definition -
vcfc:ReservedFormat_PL Declared Term Format PL reserved field definition -
vcfc:ReservedFormat_PP Declared Term Format PP reserved field definition -
vcfc:ReservedFormat_PQ Declared Term Format PQ reserved field definition -
vcfc:ReservedFormat_PS Declared Term Format PS reserved field definition -
vcfc:ReservedFormat_PSL Declared Term Format PSL reserved field definition -
vcfc:ReservedFormat_PSO Declared Term Format PSO reserved field definition -
vcfc:ReservedFormat_PSQ Declared Term Format PSQ reserved field definition -
vcfc:ReservedInfo_1000G Declared Term Info 1000G reserved field definition -
vcfc:ReservedInfo_AA Declared Term Info AA reserved field definition -
vcfc:ReservedInfo_AC Declared Term Info AC reserved field definition -
vcfc:ReservedInfo_AD Declared Term Info AD reserved field definition -
vcfc:ReservedInfo_ADF Declared Term Info ADF reserved field definition -
vcfc:ReservedInfo_ADR Declared Term Info ADR reserved field definition -
vcfc:ReservedInfo_AF Declared Term Info AF reserved field definition -
vcfc:ReservedInfo_AN Declared Term Info AN reserved field definition -
vcfc:ReservedInfo_BKPTID Declared Term Info BKPTID reserved field definition -
vcfc:ReservedInfo_BQ Declared Term Info BQ reserved field definition -
vcfc:ReservedInfo_CICN Declared Term Info CICN reserved field definition -
vcfc:ReservedInfo_CIEND Declared Term Info CIEND reserved field definition -
vcfc:ReservedInfo_CIGAR Declared Term Info CIGAR reserved field definition -
vcfc:ReservedInfo_CILEN Declared Term Info CILEN reserved field definition -
vcfc:ReservedInfo_CIPOS Declared Term Info CIPOS reserved field definition -
vcfc:ReservedInfo_CIRB Declared Term Info CIRB reserved field definition -
vcfc:ReservedInfo_CIRUC Declared Term Info CIRUC reserved field definition -
vcfc:ReservedInfo_CN Declared Term Info CN reserved field definition -
vcfc:ReservedInfo_DB Declared Term Info DB reserved field definition -
vcfc:ReservedInfo_DBRIPID Declared Term Info DBRIPID reserved field definition -
vcfc:ReservedInfo_DBVARID Declared Term Info DBVARID reserved field definition -
vcfc:ReservedInfo_DGVID Declared Term Info DGVID reserved field definition -
vcfc:ReservedInfo_DP Declared Term Info DP reserved field definition -
vcfc:ReservedInfo_END Declared Term Info END reserved field definition -
vcfc:ReservedInfo_EVENT Declared Term Info EVENT reserved field definition -
vcfc:ReservedInfo_EVENTTYPE Declared Term Info EVENTTYPE reserved field definition -
vcfc:ReservedInfo_H2 Declared Term Info H2 reserved field definition -
vcfc:ReservedInfo_H3 Declared Term Info H3 reserved field definition -
vcfc:ReservedInfo_HOMLEN Declared Term Info HOMLEN reserved field definition -
vcfc:ReservedInfo_HOMSEQ Declared Term Info HOMSEQ reserved field definition -
vcfc:ReservedInfo_IMPRECISE Declared Term Info IMPRECISE reserved field definition -
vcfc:ReservedInfo_MATEID Declared Term Info MATEID reserved field definition -
vcfc:ReservedInfo_MEINFO Declared Term Info MEINFO reserved field definition -
vcfc:ReservedInfo_METRANS Declared Term Info METRANS reserved field definition -
vcfc:ReservedInfo_MQ Declared Term Info MQ reserved field definition -
vcfc:ReservedInfo_MQ0 Declared Term Info MQ0 reserved field definition -
vcfc:ReservedInfo_NOVEL Declared Term Info NOVEL reserved field definition -
vcfc:ReservedInfo_NS Declared Term Info NS reserved field definition -
vcfc:ReservedInfo_PARID Declared Term Info PARID reserved field definition -
vcfc:ReservedInfo_RB Declared Term Info RB reserved field definition -
vcfc:ReservedInfo_RN Declared Term Info RN reserved field definition -
vcfc:ReservedInfo_RUB Declared Term Info RUB reserved field definition -
vcfc:ReservedInfo_RUC Declared Term Info RUC reserved field definition -
vcfc:ReservedInfo_RUL Declared Term Info RUL reserved field definition -
vcfc:ReservedInfo_RUS Declared Term Info RUS reserved field definition -
vcfc:ReservedInfo_SB Declared Term Info SB reserved field definition -
vcfc:ReservedInfo_SOMATIC Declared Term Info SOMATIC reserved field definition -
vcfc:ReservedInfo_SVCLAIM Declared Term Info SVCLAIM reserved field definition -
vcfc:ReservedInfo_SVLEN Declared Term Info SVLEN reserved field definition -
vcfc:ReservedInfo_SVTYPE Declared Term Info SVTYPE reserved field definition -
vcfc:ReservedInfo_VALIDATED Declared Term Info VALIDATED reserved field definition -
vcfc:SequenceAfterLeftBracket Declared Term sequence after left bracket The [p[t breakend form.
vcfc:SequenceAfterRightBracket Declared Term sequence after right bracket The ]p]t breakend form.
vcfc:SequenceBeforeLeftBracket Declared Term sequence before left bracket The t[p[ breakend form.
vcfc:SequenceBeforeRightBracket Declared Term sequence before right bracket The t]p] breakend form.
vcfc:SimpleIndelPadding Declared Term simple insertion or deletion 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 Declared Term String The VCF String type, used for a textual value whose permitted content is further constrained by the field in which it occurs.
vcfc:SymbolicAllele Declared Term symbolic allele An angle-bracketed symbolic ALT identifier such as <DEL>.
vcfc:SymbolicAllelePadding Declared Term symbolic alternate allele 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 Declared Term CNV symbolic allele type -
vcfc:SymbolicDeletion Declared Term DEL symbolic allele type -
vcfc:SymbolicDuplication Declared Term DUP symbolic allele type -
vcfc:SymbolicInsertion Declared Term INS symbolic allele type -
vcfc:SymbolicInversion Declared Term INV symbolic allele type -
vcfc:SymbolicMobileElementDeletion Declared Term DEL:ME symbolic allele subtype -
vcfc:SymbolicMobileElementInsertion Declared Term INS:ME symbolic allele subtype -
vcfc:SymbolicTandemDuplication Declared Term DUP:TANDEM symbolic allele subtype -
vcfc:SymbolicTandemRepeat Declared Term CNV:TR symbolic allele subtype -
vcfc:Unphased Declared Term unphased -
vcfc:UnspecifiedAllele Declared Term unspecified allele The <*> or <NON_REF> ALT form used to indicate an unspecified alternate allele.
vcfc:UnspecifiedAlleleNoPadding Declared Term unspecified allele, no padding 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 Declared Term VCF Float 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 Declared Term VCF Integer A signed 32-bit VCF Integer excluding -2147483648 through -2147483641, which VCF 4.5 reserves because BCF cannot encode them.
vcfc:VCFTextVector Declared Term VCF text vector encoding 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.