VCF-RDFizer Vocabulary Reference
Normative term documentation for the vcfr: namespace. This page covers classes,
properties, and alignment points to external ontologies for representing VCF files, records,
and per-sample calls in RDF.
Namespace:
https://w3id.org/vcf-rdfizer/vocab#
29 classes
11 object properties
31 datatype properties
1 annotation property
Class Hierarchy
This hierarchy summarizes the core design: file/header representation, record/call structure, and typed definitions for INFO/FORMAT/FILTER/ALT metadata.
Raw hierarchy is serialized in RDF 1.1 Turtle (TTL), generated from
ontology/vcf-rdfizer-vocabulary.ttl and loaded from assets/ontology-hierarchy.ttl.
Loading generated hierarchy TTL...Classes
| Term | Label | Description | Subclass Of | External Usage |
|---|---|---|---|---|
| vcfr:VCFFile | VCF file | VCF file artifact containing one header and zero or more VCF records. | dcat:Distribution, prov:Entity | DCATPROV-O |
| vcfr:VCFHeader | VCF header | Container for structured VCF header lines. | - | - |
| vcfr:HeaderLine | VCF header line | One structured VCF header line such as ##INFO or ##contig. |
- | - |
| vcfr:FileFormatHeaderLine | fileformat header line | Specialized header line for ##fileformat. |
vcfr:HeaderLine |
- |
| vcfr:FileDateHeaderLine | fileDate header line | Specialized header line for ##fileDate. |
vcfr:HeaderLine |
- |
| vcfr:SourceHeaderLine | source header line | Specialized header line for ##source. |
vcfr:HeaderLine |
- |
| vcfr:ReferenceHeaderLine | reference header line | Specialized header line for ##reference. |
vcfr:HeaderLine |
- |
| vcfr:ContigHeaderLine | contig header line | Structured representation of ##contig=<...> metadata. |
vcfr:HeaderLine |
- |
| vcfr:INFOHeaderLine | INFO header line | Structured representation of ##INFO=<...> definition metadata. |
vcfr:HeaderLine |
- |
| vcfr:FORMATHeaderLine | FORMAT header line | Structured representation of ##FORMAT=<...> definition metadata. |
vcfr:HeaderLine |
- |
| vcfr:FILTERHeaderLine | FILTER header line | Structured representation of ##FILTER=<...>. |
vcfr:HeaderLine |
- |
| vcfr:ALTHeaderLine | ALT header line | Structured representation of symbolic ALT allele metadata from ##ALT=<...>. |
vcfr:HeaderLine |
- |
| vcfr:VCFRecord | VCF record | One VCF row (CHROM, POS, ID, REF, ALT, and associated call-level data). | prov:Entity | PROV-O |
| vcfr:VariantCall | variant call | Call-level representation of QUAL, FILTER, INFO, FORMAT, and sample calls. | prov:Entity | PROV-O |
| vcfr:SampleCall | sample call | Per-sample call values for a variant call (for example GT, DP, AD). | prov:Entity | PROV-O |
| vcfr:FieldDefinition | field definition | Superclass for INFO, FORMAT, FILTER, and ALT definition lines. | vcfr:HeaderLine |
- |
| vcfr:InfoFieldDefinition | INFO field definition | Definition line for INFO keys. | vcfr:FieldDefinition, vcfr:INFOHeaderLine |
- |
| vcfr:FormatFieldDefinition | FORMAT field definition | Definition line for FORMAT keys. | vcfr:FieldDefinition, vcfr:FORMATHeaderLine |
- |
| vcfr:FilterDefinition | FILTER definition | Definition line for FILTER identifiers. | vcfr:FieldDefinition, vcfr:FILTERHeaderLine |
- |
| vcfr:AltDefinition | ALT definition | Definition line for symbolic ALT alleles. | vcfr:FieldDefinition, vcfr:ALTHeaderLine |
- |
| vcfr:InfoFieldValue | INFO field value | Structured key/value node for a single INFO attribute in a call. | - | - |
| vcfr:FormatFieldValue | FORMAT field value | Structured key/value node for a single FORMAT attribute in a sample call. | - | - |
| vcfr:VCFValueType | VCF value type | Enumeration superclass for VCF Type values in INFO/FORMAT definitions. |
- | - |
| vcfr:IntegerType | Integer | Enumeration value for integer typed fields. | vcfr:VCFValueType |
- |
| vcfr:FloatType | Float | Enumeration value for decimal/float typed fields. | vcfr:VCFValueType |
- |
| vcfr:FlagType | Flag | Enumeration value for boolean-style flag fields. | vcfr:VCFValueType |
- |
| vcfr:CharacterType | Character | Enumeration value for single-character fields. | vcfr:VCFValueType |
- |
| vcfr:StringType | String | Enumeration value for string fields. | vcfr:VCFValueType |
- |
| vcfr:VCFNumberArity | VCF Number arity | Represents VCF Number patterns (for example 1, A, R, G, .). |
- | - |
Object Properties
| Term | Domain | Range | Intent | External Usage |
|---|---|---|---|---|
| vcfr:hasHeader | vcfr:VCFFile |
vcfr:VCFHeader |
Connects a file artifact to its structured header container. | - |
| vcfr:hasHeaderLine | vcfr:VCFHeader |
vcfr:HeaderLine |
Attaches any concrete header line instance to a VCF header. | - |
| vcfr:hasRecord | vcfr:VCFFile |
vcfr:VCFRecord |
Connects a file to its rows (VCF records). | - |
| vcfr:hasCall | vcfr:VCFRecord |
vcfr:VariantCall |
Connects a row-level record to a call-level representation. | - |
| vcfr:hasSampleCall | vcfr:VariantCall |
vcfr:SampleCall |
Connects a call to per-sample call nodes. | - |
| vcfr:hasInfoValue | vcfr:VariantCall |
vcfr:InfoFieldValue |
Attaches structured INFO values to a variant call. | - |
| vcfr:hasFormatValue | vcfr:SampleCall |
vcfr:FormatFieldValue |
Attaches structured FORMAT values to a sample call. | - |
| vcfr:declaredBy | Not constrained in ontology | vcfr:FieldDefinition |
Links INFO/FORMAT/FILTER/ALT usage nodes to the matching header definition. | - |
| vcfr:chromosome | Not constrained in ontology | vcfr:ContigHeaderLine |
References the contig context for a CHROM value. | Comment recommends FALDO-compatible references. |
| vcfr:asSequenceAlteration | Not constrained in ontology | so:0001059 | Bridges VCF-centric entities to external sequence alteration representations. | SOSB/gvar alignment |
| vcfr:fieldType | vcfr:FieldDefinition |
vcfr:VCFValueType |
Declares the VCF Type enum for INFO/FORMAT definitions. | - |
Datatype Properties
Grouped by modeling concern to keep implementation and query logic predictable.
Domain notes:
vcfr:fieldValue, vcfr:fieldValueInteger,
vcfr:fieldValueDecimal, and vcfr:fieldValueBoolean use rdf:Resource
as domain to allow both INFO and FORMAT value nodes to share the same property set.
| Term | Domain | Range | Intent |
|---|---|---|---|
| vcfr:headerKey | vcfr:HeaderLine | xsd:string | Header key token for generic header modeling. |
| vcfr:headerValue | vcfr:HeaderLine | xsd:string | Header value token for generic header modeling. |
| vcfr:fileFormat | vcfr:VCFFile | xsd:string | VCF version string (for example VCFv4.2). |
| vcfr:fileDate | vcfr:VCFFile | xsd:date | File date header value. |
| vcfr:sourceSoftware | vcfr:VCFFile | xsd:string | Source tool/pipeline identifier. |
| vcfr:referenceGenome | vcfr:VCFFile | xsd:string | Reference genome descriptor string. |
| vcfr:contigCount | vcfr:VCFFile | xsd:integer | Optional count of declared contigs. |
| vcfr:contigId | vcfr:ContigHeaderLine | xsd:string | Contig identifier from ##contig. |
| vcfr:contigLength | vcfr:ContigHeaderLine | xsd:integer | Contig length metadata. |
| vcfr:contigAssembly | vcfr:ContigHeaderLine | xsd:string | Assembly string for a contig declaration. |
| vcfr:contigMd5 | vcfr:ContigHeaderLine | xsd:string | MD5 hash value from the contig header line. |
| vcfr:fieldId | vcfr:FieldDefinition | xsd:string | INFO/FORMAT/FILTER/ALT field identifier. |
| vcfr:fieldNumber | vcfr:FieldDefinition | xsd:string | VCF Number token (0, 1, A, R, G, .). |
| vcfr:fieldDescription | vcfr:FieldDefinition | xsd:string | Natural-language definition text. |
| vcfr:filterId | vcfr:FilterDefinition | xsd:string | FILTER-specific identifier. |
| vcfr:altId | vcfr:AltDefinition | xsd:string | ALT-specific identifier for symbolic alleles. |
| vcfr:chrom | vcfr:VCFRecord | xsd:string | CHROM column value. |
| vcfr:pos | vcfr:VCFRecord | xsd:integer | POS column value. |
| vcfr:recordId | vcfr:VCFRecord | xsd:string | ID column value (if present). |
| vcfr:ref | vcfr:VCFRecord | xsd:string | REF allele. |
| vcfr:alt | vcfr:VCFRecord | xsd:string | ALT allele string. |
| vcfr:qual | vcfr:VariantCall | xsd:decimal | QUAL score. |
| vcfr:filter | vcfr:VariantCall | xsd:string | FILTER value(s), optionally repeated as multiple literals. |
| vcfr:infoRaw | vcfr:VariantCall | xsd:string | Raw INFO column text. |
| vcfr:formatRaw | vcfr:VariantCall | xsd:string | Raw FORMAT column text. |
| vcfr:fieldValue | rdf:Resource | xsd:string | String literal payload for generic values. |
| vcfr:fieldValueInteger | rdf:Resource | xsd:integer | Typed integer payload. |
| vcfr:fieldValueDecimal | rdf:Resource | xsd:decimal | Typed decimal payload. |
| vcfr:fieldValueBoolean | rdf:Resource | xsd:boolean | Typed boolean payload. |
| vcfr:sampleId | vcfr:SampleCall | xsd:string | Sample identifier for a sample-call node. |
Annotation Properties
| Term | Purpose | Current Assertion |
|---|---|---|
| vcfr:recommendedSequenceAlterationClass | Declares recommended external class usage for sequence-alteration alignment. | vcfr:recommendedSequenceAlterationClass vcfr:recommendedSequenceAlterationClass so:0001059 . |
SHACL Validation Shapes
The SHACL profile in shacl/vcf-rdfizer-vocabulary.shacl.ttl defines structural checks
for the core graph pattern. It validates class-specific requirements while still allowing incremental
conversion workflows (for example optional call details).
Current profile highlights: 9 node shapes and
explicit support for typed null literals via
vcfr:Null on selected fields.
| Node Shape | Targets | Required / constrained terms | Purpose |
|---|---|---|---|
vcfr:VCFFileShape |
vcfr:VCFFile |
vcfr:hasHeader exactly 1, vcfr:fileFormat required; optional vcfr:fileDate, vcfr:referenceGenome, vcfr:hasRecord |
Ensures every file resource has a valid header/file metadata baseline. |
vcfr:VCFHeaderShape |
vcfr:VCFHeader |
vcfr:hasHeaderLine at least one |
Prevents empty header containers. |
vcfr:InfoFieldDefinitionShape |
vcfr:InfoFieldDefinition |
vcfr:fieldId, vcfr:fieldNumber, vcfr:fieldDescription required |
Requires complete INFO definition metadata. |
vcfr:FormatFieldDefinitionShape |
vcfr:FormatFieldDefinition |
vcfr:fieldId, vcfr:fieldNumber, vcfr:fieldDescription required |
Requires complete FORMAT definition metadata. |
vcfr:VCFRecordShape |
vcfr:VCFRecord |
Required: vcfr:chrom, vcfr:pos, vcfr:ref, vcfr:alt; optional vcfr:hasCall, vcfr:asSequenceAlteration |
Validates row-level record integrity and optional external alignment bridge. |
vcfr:VariantCallShape |
vcfr:VariantCall |
Optional vcfr:qual and vcfr:filter accept xsd values or vcfr:Null; optional links to INFO/sample values |
Supports both populated and sparse call payloads with semantic nulls. |
vcfr:SampleCallShape |
vcfr:SampleCall |
vcfr:sampleId required; optional vcfr:hasFormatValue |
Enforces sample identity while allowing variable FORMAT coverage. |
vcfr:InfoFieldValueShape |
vcfr:InfoFieldValue |
Optional vcfr:fieldValue typed as xsd:string or vcfr:Null; optional vcfr:declaredBy |
Validates typed INFO value nodes without requiring a rigid minimum field set. |
vcfr:FormatFieldValueShape |
vcfr:FormatFieldValue |
Optional vcfr:fieldValue typed as xsd:string or vcfr:Null; optional vcfr:declaredBy |
Same value-node pattern as INFO, specialized for FORMAT payloads. |
External Ontology Usage
External ontologies are used explicitly for compatibility instead of duplicating mature concepts. The table below documents where and how each reference is used.
| Ontology / Resource | Namespace | Usage in this vocabulary | VCF-RDFizer terms involved |
|---|---|---|---|
| DCAT | http://www.w3.org/ns/dcat# | Models VCF files as dataset distributions. | vcfr:VCFFile rdfs:subClassOf dcat:Distribution |
| PROV-O | http://www.w3.org/ns/prov# | Treats core resources as provenance-aware entities. | vcfr:VCFFile, vcfr:VCFRecord, vcfr:VariantCall, vcfr:SampleCall |
| Sequence Ontology (SO) | http://purl.obolibrary.org/obo/SO_ | Aligns variant representation to sequence alteration semantics. | vcfr:asSequenceAlteration range so:0001059; vcfr:recommendedSequenceAlterationClass assertion to so:0001059 |
| FALDO | http://biohackathon.org/resource/faldo# | Referenced as preferred position/reference alignment model in comments. | vcfr:chromosome comment guidance |
| GENO | http://purl.obolibrary.org/obo/GENO_ | Declared prefix for downstream alignment with genomic variant semantics. | Ontology header / namespace declarations |
| SIO | http://semanticscience.org/resource/SIO_ | Declared prefix for downstream semantic interoperability. | Ontology header / namespace declarations |
| SB/gvar (reference model) | https://swat4hcls-2025-genomic-variation.github.io/genomic-variant-schema/ | Primary alignment target for sequence alteration representation. | vcfr:asSequenceAlteration and ontology-level rdfs:seeAlso |
| HERO Genomics Ontology | https://hereditary.dei.unipd.it/ontology/genomics/ | Secondary external reference in ontology metadata. | Ontology-level rdfs:seeAlso |
VCF Crosswalk
This mapping is useful when building converters and test fixtures.
| VCF Part | Primary Terms | Notes |
|---|---|---|
| File artifact | vcfr:VCFFile, vcfr:hasHeader, vcfr:hasRecord |
Top-level node for a VCF document and its contents. |
| Header lines | vcfr:VCFHeader, vcfr:HeaderLine, specialized subclasses |
Each structured header line can carry key/value and type-specific metadata. |
| Record columns | vcfr:chrom, vcfr:pos, vcfr:recordId, vcfr:ref, vcfr:alt |
Represents the VCF row core. |
| Call-level fields | vcfr:qual, vcfr:filter, vcfr:infoRaw, vcfr:hasInfoValue |
Supports raw and structured INFO representations. |
| Sample columns | vcfr:hasSampleCall, vcfr:sampleId, vcfr:hasFormatValue |
Captures per-sample FORMAT payloads with typed value options. |
| External variant model | vcfr:asSequenceAlteration, vcfr:recommendedSequenceAlterationClass |
Bridge to so:0001059-based external models such as SB/gvar. |