Phenopacket-tools: Building and validating GA4GH Phenopackets

Journal Article · Wed May 17 00:00:00 EDT 2023 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0285433· OSTI ID:2234216

Danis, Daniel ^[1]; Jacobsen, Julius B. ^[2]; Wagner, Alex H. ^[3]; Groza, Tudor ^[4]; Beckwith, Martha A. ^[1]; Rekerle, Lauren ^[1]; Carmody, Leigh C. ^[1]; Reese, Justin ^[5]; Hegde, Harshad ^[5]; Ladewig, Markus S. ^[6]; Seitz, Berthold ^[7]; Munoz-Torres, Monica ^[8]; Harris, Nomi L. ^[5]; Rambla, Jordi ^[9]; Baudis, Michael ^[10]; Mungall, Christopher J. ^[5]; Haendel, Melissa A. ^[8]; Robinson, Peter N. ^[11]

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1. Jackson Laboratory for Genomic Medicine, Farmington, CT (United States)
2. Queen Mary Univ. of London (United Kingdom)
3. The Ohio State Univ., Columbus, OH (United States); Nationwide Children’s Hospital, Columbus, OH (United States)
4. European Bioinformatics Institute (EMBL-EBI), Cambridge (United Kingdom)
5. Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
6. Klinikum Saarbrücken (Germany)
7. Saarland University Medical Center, Homburg/Saar (Germany)
8. University of Colorado Anschutz Medical Campus, Aurora, CO (United States)
9. Barcelona Institute of Science and Technology (BIST)(Spain)
10. Univ. of Zurich (Switzerland); Swiss Inst. of Bioformatics, Zurich (Switzerland)
11. Jackson Laboratory for Genomic Medicine, Farmington, CT (United States); Univ. of Connecticut, Farmington, CT (United States)

The Global Alliance for Genomics and Health (GA4GH) is a standards-setting organization that is developing a suite of coordinated standards for genomics. The GA4GH Phenopacket Schema is a standard for sharing disease and phenotype information that characterizes an individual person or biosample. The Phenopacket Schema is flexible and can represent clinical data for any kind of human disease including rare disease, complex disease, and cancer. It also allows consortia or databases to apply additional constraints to ensure uniform data collection for specific goals. We present phenopacket-tools, an open-source Java library and command-line application for construction, conversion, and validation of phenopackets. Phenopacket-tools simplifies construction of phenopackets by providing concise builders, programmatic shortcuts, and predefined building blocks (ontology classes) for concepts such as anatomical organs, age of onset, biospecimen type, and clinical modifiers. Phenopacket-tools can be used to validate the syntax and semantics of phenopackets as well as to assess adherence to additional user-defined requirements. The documentation includes examples showing how to use the Java library and the command-line tool to create and validate phenopackets. We demonstrate how to create, convert, and validate phenopackets using the library or the command-line application. Source code, API documentation, comprehensive user guide and a tutorial can be found at https://github.com/phenopackets/phenopacket-tools. The library can be installed from the public Maven Central artifact repository and the application is available as a standalone archive. The phenopacket-tools library helps developers implement and standardize the collection and exchange of phenotypic and other clinical data for use in phenotype-driven genomic diagnostics, translational research, and precision medicine applications.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES)
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 2234216
• Journal Information: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 5 Vol. 18; ISSN 1932-6203
• Publisher: Public Library of Science
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES