Phenopacket-tools library published in PLoS One

Monarch Initiative
2 min readJul 6, 2023

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The GA4GH Phenopacket schema, designed by members of the Monarch Initiative and Phenomics First CEGS teams within the GA4GH Clin/Pheno workstream, is a widely-used standard for sharing disease and phenotype information that characterizes an individual person or biosample. It standardizes the collection and exchange of phenotypic and other clinical data for use in phenotype-driven genomic diagnostics, translational research, and precision medicine applications. About a million phenopackets have been created to date by organizations all over the world, including the European Joint Programme on Rare Diseases and Japan’s biobank network. The GA4GH Phenopacket standard was accepted by ISO in August 2022.

A recent paper in PLoS One, led by Daniel Danis, describes the phenopacket-tools library for working with phenopackets. Phenopacket-tools (https://github.com/phenopackets/phenopacket-tools) is an open-source Java library and command-line application for the construction, conversion from V1 to V2, and validation of phenopackets. The PLoS One paper highlights the use of phenopackets-tools for collecting, quality-checking, and exchanging data related to rare diseases, helping to support medical research and progress in the fight against rare diseases.

Figure: An overview of validation errors. Phenopacket-tools includes multiple off-the-shelf validators for performing basic and domain-specific checks. The validators emit errors that refer to invalid phenopacket components. This table lists the errors and solutions for issues discovered in example phenopackets that are included in the phenopacket-tools distribution.

Further reading

PLoS One article about phenopacket-tools: Danis D, Jacobsen JOB, Wagner AH, Groza T, Beckwith MA, Rekerle L, Carmody LC, Reese J, Hegde H, Ladewig MS, Seitz B, Munoz-Torres M, Harris NL, Rambla J, Baudis M, Mungall CJ, Haendel MA, Robinson PN. Phenopacket-tools: Building and validating GA4GH Phenopackets. PLoS One. 2023 May 17;18(5):e0285433. http://dx.doi.org/10.1371/journal.pone.0285433 PMCID: PMC10191354

More about using phenopackets: Ladewig MS, Jacobsen JOB, Wagner AH, Danis D, El Kassaby B, Gargano M, Groza T, Baudis M, Steinhaus R, Seelow D, Bechrakis NE, Mungall CJ, Schofield PN, Elemento O, Smith L, McMurry JA, Munoz-Torres M, Haendel MA, Robinson PN. GA4GH phenopackets: A practical introduction. Advanced Genetics. Wiley; 2022 Aug 25;2200016. https://onlinelibrary.wiley.com/doi/10.1002/ggn2.202200016

Press release: CU Data Scientists Develop Rare Disease Phenopacket Standard, Tools For Global Use. https://news.cuanschutz.edu/dbmi/cu-data-scientists-develop-rare-disease-phenopacket-standard-tools-for-global-use

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