Phenopacket-tools: Building and validating GA4GH Phenopackets

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  • dc.contributor.author Danis, Daniel
  • dc.contributor.author Jacobsen, Julius O.B.
  • dc.contributor.author Wagner, Alex H.
  • dc.contributor.author Groza, Tudor
  • dc.contributor.author Beckwith, Martha A.
  • dc.contributor.author Rekerle, Lauren
  • dc.contributor.author Carmody, Leigh C.
  • dc.contributor.author Reese, Justin
  • dc.contributor.author Hegde, Harshad
  • dc.contributor.author Ladewig, Markus S.
  • dc.contributor.author Seitz, Berthold
  • dc.contributor.author Muñoz-Torres, Mónica
  • dc.contributor.author Harris, Nomi L.
  • dc.contributor.author Rambla de Argila, Jordi
  • dc.contributor.author Baudis, Michael
  • dc.contributor.author Mungall, Christopher J.
  • dc.contributor.author Haendel, Melissa A.
  • dc.contributor.author Robinson, Peter N.
  • dc.date.accessioned 2023-06-26T05:54:28Z
  • dc.date.available 2023-06-26T05:54:28Z
  • dc.date.issued 2023
  • dc.description.abstract 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.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation 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. DOI: 10.1371/journal.pone.0285433
  • dc.identifier.doi http://dx.doi.org/10.1371/journal.pone.0285433
  • dc.identifier.issn 1932-6203
  • dc.identifier.uri http://hdl.handle.net/10230/57321
  • dc.language.iso eng
  • dc.publisher Public Library of Science (PLoS)
  • dc.relation.ispartof PLoS One. 2023 May 17;18(5):e0285433
  • dc.rights © 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.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Ontologies
  • dc.subject.keyword Genomics
  • dc.subject.keyword Renal cancer
  • dc.subject.keyword Lung and intrathoracic tumors
  • dc.subject.keyword Diagnostic medicine
  • dc.subject.keyword Metadata
  • dc.subject.keyword Phenotypes
  • dc.subject.keyword Syntax
  • dc.title Phenopacket-tools: Building and validating GA4GH Phenopackets
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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Articles (Center for Genomic Regulation (CRG))