VCF Core Vocabulary
A semantic companion for publishing VCF files, structured headers, records, call assessments, and sample-level values as interoperable RDF.
Ontology Snapshot
Counts are generated from the source Turtle ontology.
Represent VCF Data with Context
VCF Core preserves the file-level provenance and header declarations that make a VCF interpretable, then represents its records, call assessments, INFO annotations, FORMAT fields, and sample values as linked RDF resources. It is designed for bioinformaticians implementing transformations, data stewards publishing interoperable variant data, and ontology developers aligning VCF calls with broader genomics models.
Vocabulary Reference
For ontology developers and RDF users: learn the classes, properties, hierarchy, and external alignments.
Open ReferenceRelationship Graph
For data integrators and VCF users: see how files, headers, records, calls, and values connect.
Open GraphCore Terms
The central classes and properties used to represent VCF files, headers, records, calls, and field values.
vcfc:VCFFile
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
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:VCFRecord
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:VariantCall
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:SampleCall
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:hasRecord
Associates a VCF file with one of its tab-delimited data records.
Example Explorer
Inspect the raw VCF and serialized RDF examples without leaving the companion site.
Loading example...Vocabulary Scope
VCF Core is intentionally VCF-centric: it captures the syntax-facing file, header, record, and per-sample call information that is commonly lost when only a sequence alteration is modelled.
- Use VCFFile, VCFHeader, and HeaderLine to preserve the source artifact and its declarations.
- Use VCFRecord, VariantCall, and SampleCall to represent a data line and its call-level or sample-level values.
- Use asSequenceAlteration to link a VCF-centric representation to an external sequence-alteration model when needed.
Suggested Canonical IRI Pattern
The site provides suggested instance IRIs for generating RDF from VCF files. The templates are also formalized by vcfc:iriTemplate in the ontology. The examples use portable local identifiers such as file://example-file1.vcf#header; use an absolute file:///... form for a real local path or a stable HTTP(S) base when resources must be shared and dereferenced.
- VCFFile file://{vcfFilePath}
- VCFHeader file://{vcfFilePath}#header
- HeaderLine file://{vcfFilePath}#header/line/{lineId}
- VCFRecord file://{vcfFilePath}#record/{recordKey}
- VariantCall file://{vcfFilePath}#call/{recordKey}
- SampleCall file://{vcfFilePath}#sample/{recordKey}/{sampleId}
- InfoFieldValue file://{vcfFilePath}#call/{recordKey}/info/{fieldKey}
- FormatFieldValue file://{vcfFilePath}#sample/{recordKey}/{sampleId}/fmt/{fieldKey}