Phenotype-Associated Variants in Saudi Arabia

PAVS: Phenotype-Associated Variants in Saudi Arabia PAVS (Phenotype-Associated Variants in Saudi Arabia) is a curated genotype–phenotype database integrating rare disease case data from Saudi Arabian clinical cohorts, mixed-population cohorts, and literature-derived phenopackets. All cases are encoded as GA4GH Phenopackets v2.0 and integrated into an RDF knowledge graph using the PAVS ontology, HPO, OMIM, and related biomedical vocabularies. This archive contains: PAVS cases TSV (PAVS_cases.tsv): A flat, tab-separated table of all 7,510 clinical cases. Each row contains case ID, cohort source, sex, consanguinity, family history, solved status, disease, gene, variant (HGVS + VCF), zygosity, ACMG classification, VEP consequence, gnomAD scores, and HPO terms. Suitable for direct use in R, Python, or Excel. PAVS phenopackets (combined and individual): 7,510 clinical cases in GA4GH Phenopackets v2.0 format, comprising 5,132 Saudi clinical cases, 522 mixed-population clinical cases (Ziats et al.), and 1,856 DDD clinical cases. Note: Literature phenopackets (9,588 cases from the Phenopackets Store) are included in the RDF knowledge graph (literature.ttl) but are not redistributed as individual JSON files here; they remain available at https://github.com/monarch-initiative/phenopacket-store. RDF knowledge graph (Turtle format): Six named graphs covering cases, gene records, HPO annotation data, HPO information content, literature phenopackets, and dataset metadata, totaling approximately 18.7 million RDF triples. Designed for deployment in OpenLink Virtuoso (SPARQL 1.1 endpoint). VoID dataset description (void.ttl): W3C VoID vocabulary metadata describing the knowledge graph, its named graphs, and 28 external linksets to reference ontologies and databases. Manually curated case data (XLSX): Source spreadsheet for the 1,422 manually curated Saudi cases (M-cohort), prior to phenotype normalization and phenopacket conversion. Links and Resources: Live Instance & SPARQL Endpoint: https://pavs.phenomebrowser.net Code Repository (Web UI, API, Processing): https://github.com/bio-ontology-research-group/pavs Arabic HPO Translation: https://doi.org/10.5281/zenodo.19311231 Related Publication: This dataset accompanies the manuscript:"PAVS: Phenotype-Associated Variants in Saudi Arabia" (submitted).