Phenopackets Implementation Resources

Recommended ontologies for use with Phenopackets

Here, we provide general recommendations for ontologies that we have found to be useful.

Example Code

Here we provide several examples that demonstrate how to work with Phenopackets in Java and C++. There are also Python examples in the source code test directory. All three language implementations are automatically produced as part of the build (Java Build).

Phenopackets Tools

An app and library for building, conversion, and validation of GA4GH Phenopackets. The documentation includes a Tutorial showing how to use the CLI, a comprehensive CLI user guide, a Library user guide, and the Javadoc API documentation.

OMOP Exporter

Export Phenopackets from OMOP. This tool was developed as part of the Biohackathon Europe 2021 by members of Project 36.

Phenopacket-FHIR Implementation Guide

This implementation guide is a set of rules about how FHIR resources are used (or should be used) to implement Phenopackets in an EHR setting. The focus of this IG is to support rare disease use cases.