Welcome to phenopacket-tools’s documentation!
The Phenopacket Schema of the Global Alliance for Genomics and Health (GA4GH) was approved by the GA4GH in 2022 and additional certified by the International Standards Organization (ISO) as ISO 4454:2022. A description of the schema was published in Jacobsen JOB, et al. 2022 and a detailed tutorial appeared in Ladewig et al., 2022.
A Phenopacket characterizes an individual person or biosample, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. The Phenopacket schema supports the FAIR principles (findable, accessible, interoperable, and reusable), and computability. Specifically, Phenopackets are designed to be both human and machine-interpretable, enabling computing operations and validation on the basis of defined relationships between diagnoses, lab measurements, and genotypic information.
Phenopacket-tools is an open-source Java library and command-line interface (CLI) application for working with GA4GH phenopackets. The library has three main goals:
To simplify creating phenopackets with Java code using streamlined builders and predefined building blocks such as units, anatomical organs, and clinical modifiers.
To convert phenopackets from the obsoleted version 1 to the version 2 (current) of the Schema.
To provide a validation framework for checking phenopackets for syntactical and semantic correctness and to enable developers to extend the validation framework to encode the specific requirements of consortia or projects using either JSON schema or programmatic tools.
On top of the library, we provide a standalone CLI application for conversion and validation. The source code is available from our GitHub repository.
The following sections describe phenopacket-tools library and CLI application. We start with Tutorial to provide a quick overview of the CLI functionality. We follow with comprehensive description of the Command-line interface. The rest of the documentation offers an in-depth user guide and a showcase of the library functionality in JVM-based applications.
Contents:
Overview of the GA4GH Phenopacket Schema.