Phenomics Exchange for Research and Diagnostics
0.1.0 - ci-build International flag

Phenomics Exchange for Research and Diagnostics, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 0.1.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/phenomics-exchange-ig/ and changes regularly. See the Directory of published versions

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Official URL: http://hl7.org/fhir/uv/phenomics-exchange/ImplementationGuide/hl7.fhir.uv.phenomics-exchange Version: 0.1.0
Draft as of 2024-06-18 Computable Name: PhenomicsExchange

Copyright/Legal: Global Alliance for Genomics and Health

GA4GH Phenopackets

The Global Alliance for Genomics and Health (GA4GH) Phenopacket standard intends to support global exchange of computable case-level phenotypic information for all types of disease diagnosis and research. The Phenopacket standard is a freely available, community-driven standard that streamlines exchange and systematic use of phenotypic data, which will enable sophisticated computational analysis of both clinical and genomic information to help improve our understanding of diseases and our ability to manage them.

A Phenopacket represents an individual proband or patient and includes information about the individual such as age (which can be represented in multiple ways including ranges to protect privacy) and sex, any existing disease diagnoses. Almost all elements of a Phenopacket are optional. A simple Phenopacket containing only information about the proband and a list of phenotypic features is all that is required for use cases of Mendelian genomic disease diagnostics. More comprehensive Phenopackets containing additional data about biosamples and treatment may be appropriate for use cases surrounding rare disease, common/complex disease, or cancer.

The schema as well as source code in Java, C++, and Python is available from the phenopacket-schema GitHub repository.

The phenopacket schema is being developed under the auspices of the Global Alliance for Genomics and Health, GA4GH. The native version is developed using Google’s Protocol buffers, i.e., protobuf (version 3).

GA4GH 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.

Understanding FHIR (Prerequisite)

This implementation guide uses terminology, notations and design principles that are specific to FHIR. Before reading this implementation guide, its important to be familiar with some of the basic principles of FHIR as well as general guidance on how to read FHIR specifications. Readers who are unfamiliar with FHIR are encouraged to read (or at least skim) the following prior to reading the rest of this implementation guide.

This implementation guide builds on FHIR v4.0.1: R4.

Dependencies

Package hl7.fhir.uv.genomics-reporting#2.0.0

Guidelines for reporting of clinical genomics results using HL7 FHIR. (built Mon, May 9, 2022 16:52+0000+00:00)

Package hl7.fhir.uv.extensions#5.1.0-cibuild

This IG defines the global extensions - the ones defined for everyone. These extensions are always in scope wherever FHIR is being used (built Sun, Apr 21, 2024 19:45+0000+00:00)

Cross Version Analysis

This is an R4 IG. None of the features it uses are changed in R4B, so it can be used as is with R4B systems. Packages for both R4 (hl7.fhir.uv.phenomics-exchange.r4) and R4B (hl7.fhir.uv.phenomics-exchange.r4b) are available.

Global Profiles

There are no Global profiles defined

IP Statements

This publication includes IP covered under the following statements.