Short Description

This track will test the creation and exchange of phenotypic data and phenotypic patient profiles for use in genetic testing.  It will use the GA4GH/ISO Phenopacket (version 2) FHIR IG.

Long Description

Several clinical and research use cases require the creation and exchange of rich and structured phenotypic data. Such data can also be aggregated into “phenotypic profiles” for a patient based on the specific use case being addressed. For example, in the context of rare disease diagnostics and genomic analyses, it is very important to have access to the clinical/phenotypic profile of a patient in order to better interpret laboratory results of genomic sequencing.

The GA4GH Phenopacket Schema is an established model (it is also ISO certified) and toolset to represent and exchange such information in a “phenopacket”, a packet of clinical and phenotypic information to support genomic interpretation.  The Phenopackets Schema is a general framework for profiling the clinical picture of a patient for a specific use case based on existing clinical information from one or more sources. 

Over the past couple of years, there has been an interest in implementing the Phenopackets Schema and the underlying use cases in FHIR. This has resulted in the creation of the GA4GH Phenopacket (version 2) FHIR IG. This track aims to exercise this evolving IG to obtain community feedback and test existing IG-based tools. We are also collaborating with the PhenoTips vendor, a phenotypic capture tool that can send data to an EHR or clinical lab, to explore the feasibility of implementing this IG in PhenoTips in the near future.

This track has several goals and others will be added based on participation:

  • Representing phenotypic information in FHIR based on the IG, or beyond the IG if and when needed.
  • Representing phenotypic profiles.   
  • Being able to exchange phenotypic data and packets in a reliable way.
  • Relating/connecting FHIR-based phenotypic data and packets to other FHIR resources such as laboratory requests and results.
  • Converting between the GA4GH Phenopackets Schema format and the equivalent FHIR representations.
  • Understanding the possible issues with adopting the GA4GH Phenopacket (version 2) FHIR IG by existing systems such as PhenoTips


Test the design of the FHIR Resources/profiles of the GA4GH Phenopacket (version 2) FHIR Implementation Guide.

Track Prerequisites

Track Lead(s)

Shahim Essaid

Track Lead Email(s) (University of Colorado:,

Specification Information

Call for participants

  • Systems collecting or exchanging clinical information with a focus on phenotypic data and profiles.
  • Bioinformatics tools needing structured phenotypic data as input to their underlying algorithms, such as clinical diagnostic labs.
  • Workflows and providers involved in clinical or research use cases that involve genomic analysis and interpretation.
    • The GenomeX FHIR Accelerator team.

Zulip stream

Track Kick off Call

Join Zoom Meeting on 9/12/2022 at 11 am PT 2 pm ET.

Missed the call?  View the recording here

Clinical Input Required?
Related Tracks?

Testing Scenario:

Role 1: Clinician requesting a genomic analysis and attaching the phenotypic data and patient profile

The main clinical use case / workflow being tested during this track is the integration of structured phenotypic data in a clinical workflow that involves the performance of a genomic sequencing by a laboratory and the subsequent interpretation of the sequencing results by a medical geneticist.

This role will:

  • Enter or review existing phenotypic data through systems playing Roles 2 or 3.
  • Create a laboratory request to perform genomic sequencing and/or other related laboratory requests.

Role 2: Phenotypic data and phenotypic patient profile provider (PhenoTips)

This role represents a system that is able to create original phenotypic data and phenotypic patient profiles, and write them to the system playing Role 3.  This role will be played by the PhenoTips system during this track.

This role will:

  • Understand how to represent native/internal data according to the R4 Resource model.
  • Understand how to conform to the GA4GH Phenopacket (version 2) FHIR IG.
  • Create R4 and IG conforming JSON resources.
  • Write the JSON resources to the system playing Role 3.

Note: this will be simulated since this level of FHIR and IG implementation in PhenoTips is still on a future roadmap for PhenoTips. Simulating and testing the above implementation steps outside of the current PhenoTips system (but still using the current output data and formats) is till a very valuable exercise to facilitate future native implementation of FHIR and related IGs in the PhenoTips system.

Role 3: FHIR Repository

A R4 FHIR server that is the hub for data exchange. This could represent an EHR FHIR interface.

This role will:

  • Load the GA4GH Phenopacket (version 2) FHIR IG
  • Perform R4 and GA4GH Phenopacket (version 2) FHIR IG validation operations
  • REST CRUD operations for resources being exchanged as part of this track.
  • The hub for data exchange between the different other roles/scenarios testing in this track.

Role 4: Laboratory performing genomic sequencing

This role represents a laboratory performing the laboratory request sent by Role 1.

This is a stretch role. This role will likely be simulated by a few demo laboratory output files (i.e. genomic sequencing files) but this role will, as a stretch goal, attempt to make such files “accessible” through the system playing Role 3.

This role will:

  • Retrieve and perform the genomic sequencing laboratory request
  • Deposits the results in the appropriate system(s) and explore how to make them accessible through FHIR and the system playing Role 3

Role 5: Convert between GH4GA Phenopackets Schema and FHIR R4

This role will be played by tools able to convert between these two data models as an interoperability solution for downstream bioinformatics tools that have already adopted the GH4GA Phenopackets Schema but are not yet able to adopt FHIR. PhenoTips is one such example in the short term.

This role will:

  • Convert GH4GA Phenopackets Schema based files to FHIR resources
    • Conforming to the GA4GH Phenopacket (version 2) FHIR IG
  • Convert FHIR resources conforming to GA4GH Phenopacket (version 2) FHIR IG to GH4GA Phenopackets Schema based files
  • Test round tripping between the above to steps to understand lossiness and other interoperability issues between these two data models.

Role 6: Medical geneticist performing an interpretation and diagnosis

This role represents a medical geneticist using all available information to perform an interpretation and diagnosis based on the phenotypic clinical picture and the genomic sequencing results.

This is a stretch role.

This role will:

  • Retrieve available data from the system playing Role 3 and
    • Using bioinformatics tools and databases to perform the needed analysis
  • Report interpretation and diagnosis to the system playing Role 3 and attempt to conform to the following IGs:
    • GA4GH Phenopacket (version 2) FHIR IG
    • Genomics Reporting IG

Role 7: Terminology services

The biomedical informatics community has already developed data models, tools, and other resources to implement the above roles outside of FHIR. This has also led to the creating and use of several terminologies that are still not part of the well established set of terminologies being used in clinical care production systems. This terminology gap is an important barrier for implementing the above roles in FHIR and maintaining interoperability between FHIR and non-FHIR systems, especially for the biomedical research community.

This role, as a stretch role, will attempt to address this gab by demonstrating  some early efforts to bridge this gap in FHIR

This role will:

  • Provide a R4 FHIR Terminology Service instance.
  • Load one or more terminologies that are not available through the usual FHIR terminology services instances
    • The main terminology being the Human Phenotype Ontology
  • Understand the use of such terminologies in value sets and resource profiles.

The above roles are represented in the following diagram. The evolving version of this diagram can also be viewed at this link: