From VCF to RDF: RML-Based Conversion Approaches for the Semantic Representation of Variant Data

Representing Variant Call Format (VCF) data using the Resource Description Framework (RDF) offers benefits in interoperability, integration with other biomedical datasets, and selective privacy protections. Due to complexities of the data represented in VCF files, conversion of VCF to RDF poses challenges, especially concerning complex, heterogeneous data fields. Here, we propose converting VCF files to serialized RDF using the RML mapping language and established genomic data ontologies. Such a methodology will demonstrate the feasibility of an RML-based approach and inform a more FAIR, machine-actionable representation strategy for representing VCF data that is compatible with semantic data privacy policies and useful in both clinical and academic domains.

@inproceedings{crum_swat4hcls_vcfrdf_2026,
  author = {Crum, Elias and Buelens, Bart and Ertaylan, Gokhan and Taelman, Ruben},
  title = {From VCF to RDF: RML-Based Conversion Approaches for the Semantic Representation of Variant Data},
  month = mar,
  booktitle = {Proceedings of the 17th International SWAT4HCLS Conference},
  year = {2026},
  url = {https://app.oxfordabstracts.com/content/events/76267/submitters/809779/submissions/fe-d9185253-db88-43c6-a6a6-2e81a9941995/questions/132492/file/3a9a23b2-73a1-4476-811c-1217b2be1933.pdf}
}