Phenopacket-tools: Building and validating GA4GH Phenopackets.

Autor: Danis D; The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States of America., Jacobsen JOB; William Harvey Research Institute, Queen Mary University of London, London, United Kingdom., Wagner AH; Departments of Pediatrics and Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH, United States of America.; The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States of America., Groza T; EMBL-EBI, Cambridge, United Kingdom., Beckwith MA; The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States of America., Rekerle L; The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States of America., Carmody LC; The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States of America., Reese J; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America., Hegde H; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America., Ladewig MS; Department of Ophthalmology, Klinikum Saarbrücken, Saarbrücken, Germany., Seitz B; Department of Ophthalmology, Saarland University Medical Center, Homburg/Saar, Germany., Munoz-Torres M; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America., Harris NL; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America., Rambla J; European Genome-Phenome Archive (EGA) in the Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain., Baudis M; University of Zurich and Swiss Institute of Bioinformatics, Zurich, Switzerland., Mungall CJ; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America., Haendel MA; Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America., Robinson PN; The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States of America.; Institute for Systems Genomics, University of Connecticut, Farmington, CT, United States of America.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2023 May 17; Vol. 18 (5), pp. e0285433. Date of Electronic Publication: 2023 May 17 (Print Publication: 2023).
DOI: 10.1371/journal.pone.0285433
Abstrakt: 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.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2023 Danis et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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