The Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema was released in 2022 and approved by ISO as a standard for sharing clinical and genomic information about an individual, including phenotypic descriptions, numerical measurements, genetic information, diagnoses, and treatments. A phenopacket can be used as an input file for software that supports phenotype-driven genomic diagnostics and for algorithms that facilitate patient classification and stratification for identifying new diseases and treatments. There has been a great need for a collection of phenopackets to test software pipelines and algorithms. Here, we present phenopacket-store. Version 0.1.12 of phenopacket-store includes 4916 phenopackets representing 277 Mendelian and chromosomal diseases associated with 236 genes, and 2872 unique pathogenic alleles curated from 605 different publications. This represents the first large-scale collection of case-level, standardized phenotypic information derived from case reports in the literature with detailed descriptions of the clinical data and will be useful for many purposes, including the development and testing of software for prioritizing genes and diseases in diagnostic genomics, machine learning analysis of clinical phenotype data, patient stratification, and genotype-phenotype correlations. This corpus also provides best-practice examples for curating literature-derived data using the GA4GH Phenopacket Schema.

Berlin Institute of Health at Charité Universitätsmedizin Berlin Berlin Germany

Brotman Baty Institute for Precision Medicine 1959 NE Pacific Street Box 357657 Seattle WA 98195 USA

Department of Biomedical Informatics University of Colorado Anschutz Medical Ccampus

Department of Genetics and Genome Biology University of Leicester Leicester UK

Department of Genetics and Genome Sciences University of Connecticut Health Center Farmington CT USA

Department of Immunology 2nd Faculty of Medicine Charles University and University Hospital in Motol Prague Czech Republic

Department of Immunology National Institute of Women's Children's and Adolescents' Health Fernandes Figueira Rio de Janeiro Brazil

Department of Ophthalmology University Clinic Marburg Campus Fulda Fulda Germany

Department of Paediatric Immunology Great Ormond Street Hospital for Children NHS Foundation Trust London UK

Department of Pediatrics Division of Genetic Medicine Seattle Children's Hospital Seattle WA 98195 USA

Department of Pediatrics Division of Genetic Medicine University of Washington 1959 NE Pacific Street Box 357371 Seattle WA 98195 USA

Department of Pediatrics Faculty of Medicine and University Hospital Carl Gustav Carus Technische Universität Dresden Dresden Germany

Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory Berkeley CA USA

Division of Informatics Imaging and Data Science The University of Manchester Manchester UK

ELLIS European Laboratory for Learning and Intelligent Systems

High Complexity Laboratory National Institute of Women's Children's and Adolescents' Health Fernandes Figueira Rio de Janeiro Brazil

Medica Genetics University of Catania Italy

Morgagni foundation and Clinic Catania Italy

North West Thames Regional Genetics Service Northwick Park and St Mark's Hospitals London UK

Rare Care Centre Perth Children's Hospital Nedlands WA 6009 Australia

SingHealth Duke NUS Institute of Precision Medicine 5 Hospital Drive Level 9 Singapore 169609 Singapore

Telethon Kids Institute Nedlands WA 6009 Australia

The Jackson Institute for Genomic Medicine 10 Discovery Drive Farmington CT 06032 USA

University Center for Rare Diseases Faculty of Medicine and University Hospital Carl Gustav Carus Technische Universität Dresden Dresden Germany

University College London Institute of Child Health London United Kingdom

University of Leicester Leicester UK

University of North Carolina at Chapel Hill Chapel Hill NC USA

Utrecht University Utrecht the Netherlands

William Harvey Research Institute Queen Mary University of London London UK

HGG Adv. 2025 Jan 9;6(1):100371. doi: 10.1016/j.xhgg.2024.100371. PubMed

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