is a Knowledge Graph.
RDF knowledge graph from the Bio-Ontology Research Group at KAUST that represents PAVS (Phenotype-Associated Variants in Saudi Arabia), a curated database of clinical cases from Saudi Arabian rare disease cohorts. Each case links HPO-encoded phenotypes to genomic variants, genes, zygosity, pathogenicity classifications and MONDO/OMIM diagnoses, with annotations from ClinVar, ClinGen, gnomAD, Ensembl VEP, GO, GTEx and MGI. The graph also includes DDD study cases and literature phenopackets as comparators, and is served from a public Virtuoso SPARQL endpoint.
biomedical, rare disease, genetic variation, genomics, phenotype, clinical
No external IDs available
| ID | Name | URL | Category | Format | Description |
|---|---|---|---|---|---|
| pavs-kg.sparql | PAVS SPARQL Endpoint | sparql | Programming Interface | http | Public Virtuoso SPARQL endpoint for t... |
| pavs-kg.portal | PAVS Web Portal | pavs.phenomebrowser.net | Graphical Interface | http | PAVS web portal with phenotype-based ... |
| pavs-kg.api | PAVS REST API | docs | Programming Interface | http | FastAPI REST API backing the PAVS por... |
| pavs-kg.phenopackets | PAVS Phenopackets | PAVS_phenopackets.json (1.8 MB) | Product | json | Combined GA4GH Phenopackets v2 JSON f... |
| pavs-kg.code | PAVS Knowledge Graph Pipeline | pavs-knowledge-graph | Process | python | Pipeline code that normalizes source ... |
PAVS (Phenotype-Associated Variants in Saudi Arabia) is a curated database of genotype-phenotype data from Saudi Arabian rare disease patients, built by the Bio-Ontology Research Group at King Abdullah University of Science and Technology (KAUST). It combines 5,132 Saudi clinical cases from four Saudi cohorts and 522 cases from a mixed-population cohort, plus 1,856 cases from the Deciphering Developmental Disorders (DDD) study and 9,588 literature phenopackets from Phenopacket Store for comparison.
The pipeline normalizes phenotypes to the Human Phenotype Ontology, diseases to MONDO and OMIM, genotypes to GENO and variants to HGVS. It then annotates variants with Ensembl VEP, ClinVar, ClinGen, gnomAD and Saudi population allele frequencies, and annotates genes with gnomAD constraint metrics, GO annotations, GTEx expression and MGI mouse phenotypes. Cases are exported as GA4GH Phenopackets v2 and as RDF (Turtle), which is loaded into a Virtuoso triple store behind the PAVS web portal and SPARQL endpoint. Saudi cases are tagged with HANCESTRO and GAZ terms.
Pipeline code is GPL-3.0. Curated data, normalization and annotation are CC BY 4.0.
Created: October 05, 2026 | Last modified: October 05, 2026