The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Khalifa A, Krawitz PM, Koehler S, Laraway BJ, Lehvaeslaiho H, Lloyd KC, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Schofield PN, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C, Haendel MA, Robinson PN.

medRxiv, 2021.11.27.21266944. doi:10.1101/2021.11.27.21266944


Despite great strides in the development and wide acceptance of standards for exchanging structured information about genomic variants, there is no corresponding standard for exchanging phenotypic data, and this has impeded the sharing of phenotypic information for computational analysis. Here, we introduce the Global Alliance for Genomics and Health (GA4GH) Phenopacket schema, which supports exchange of computable longitudinal case-level phenotypic information for diagnosis and research of all types of disease including Mendelian and complex genetic diseases, cancer, and infectious diseases. To support translational research, diagnostics, and personalized healthcare, phenopackets are designed to be used across a comprehensive landscape of applications including biobanks, databases and registries, clinical information systems such as Electronic Health Records, genomic matchmaking, diagnostic laboratories, and computational tools. The Phenopacket schema is a freely available, community-driven standard that streamlines exchange and systematic use of phenotypic data and will facilitate sophisticated computational analysis of both clinical and genomic information to help improve our understanding of diseases and our ability to manage them.


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