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 (King Abdulaziz University Hospital, KAUH), 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).PAVS: 沙特阿拉伯表型关联变异（Phenotype-Associated Variants in Saudi Arabia） PAVS（沙特阿拉伯表型关联变异数据库，Phenotype-Associated Variants in Saudi Arabia）是一款经人工审核整理的基因型-表型数据库，整合了沙特阿拉伯临床队列、混合人群队列的罕见病病例数据，以及来自文献的表型数据包（phenopackets）。所有病例均采用GA4GH表型数据包v2.0（GA4GH Phenopackets v2.0）格式进行编码，并通过PAVS本体（PAVS ontology）、人类表型本体（Human Phenotype Ontology, HPO）、在线人类孟德尔遗传数据库（Online Mendelian Inheritance in Man, OMIM）及相关生物医学词汇表，整合为资源描述框架（Resource Description Framework, RDF）知识图谱。 本数据集归档内容包括： PAVS病例TSV文件（PAVS_cases.tsv）：一份包含全部7510例临床病例的平面制表符分隔值（Tab-Separated Values, TSV）表格。每一行涵盖病例ID、队列来源、性别、近亲婚配情况、家族病史、确诊状态、疾病、基因、变异（采用HGVS命名格式+VCF格式）、合子性、美国医学遗传学与基因组学学会（American College of Medical Genetics and Genomics, ACMG）分类、变异效应预测工具（Variant Effect Predictor, VEP）后果注释、基因组聚合数据库（Genome Aggregation Database, gnomAD）评分以及HPO术语。该文件可直接在R、Python或Excel环境中使用。 PAVS表型数据包（合并版与单例版）：包含7510例临床病例的GA4GH表型数据包v2.0格式文件，其中包括5132例沙特临床病例（来自阿卜杜勒阿齐兹国王大学医院，King Abdulaziz University Hospital, KAUH）、522例混合人群临床病例（来自Ziats等研究）以及1856例发育障碍基因型-表型数据库（Developmental Disorders Genotype-Phenotype Database, DDD）临床病例。 注意：文献来源表型数据包（来自表型数据包仓库的9588例病例）已整合至RDF知识图谱（literature.ttl）中，但未作为独立JSON文件在此分发；这些数据仍可在https://github.com/monarch-initiative/phenopacket-store获取。 RDF知识图谱（Turtle格式）：包含6个命名图，覆盖病例、基因记录、HPO注释数据、HPO信息内容、文献来源表型数据包以及数据集元数据，总计约1870万条RDF三元组。该图谱适配OpenLink Virtuoso部署，支持SPARQL 1.1端点查询。 VoID数据集描述文件（void.ttl）：采用万维网联盟（World Wide Web Consortium, W3C）的互联数据集词汇表（Vocabulary of Interlinked Datasets, VoID）元数据，用于描述该知识图谱及其命名图，以及28个指向参考本体和数据库的外部链接集。 人工审核整理的病例数据（XLSX格式）：包含1422例经人工审核整理的沙特病例（M队列）的原始电子表格，该数据未经过表型标准化处理及表型数据包格式转换。 链接与资源： 实时实例与SPARQL端点：https://pavs.phenomebrowser.net 代码仓库（包含Web界面、API、处理脚本）：https://github.com/bio-ontology-research-group/pavs 阿拉伯语HPO翻译版本：https://doi.org/10.5281/zenodo.19311231 相关研究论文： 本数据集配套的手稿为《PAVS: Phenotype-Associated Variants in Saudi Arabia》（已投稿）。