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 2024-01-17				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.

• FHIR overview
• Developer’s Introduction
• Clinical Introduction
• FHIR data types
• Using codes
• References between resources
• How to read resource and profile definitions
• Base resource

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 Wed, Dec 20, 2023 00:21+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.

• Global Alliance for Genomics and Health
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  • Karyotypic sex code system: KaryotypicSex
  • Categories: ObservationCategories
  • Section Type: Bundle/PhenopacketsBundleExample01, Composition/DevelopmentalDelay, Composition/PhenopacketCompositionExample01 and Phenopacket
• Copyright HL7. Licensed under creative commons public domain
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  • diagnosticServiceSectionId: Bundle/PhenopacketsBundleExample01, DiagnosticReport/PhenopacketsGenomicInterpretationExample01, DiagnosticReport/PhenopacketsGenomicInterpretationExample02 and PhenopacketsGenomicInterpretation
  • identifierType: Bundle/PhenopacketsBundleExample01, Patient/Proband1 and Patient/example-patient
  • degreeLicenseCertificate: Practitioner/PeterGeneticist
• Copyrights permitted under terms specified by Creative Commons Attribution 4.0 International (CC BY 4.0) .Consistent with the terms of CC BY 4.0, HL7 is permitted to share, copy and redistribute the material in any medium or format and adapt, remix, transform, and build upon the material for its purposes as long as the CC BY 4.0 license terms are upheld. HL7 must must give appropriate credit, provide a link to the license, and indicate if changes were made. HL7 may do so in any reasonable manner, but not in any way that suggests the licensor endorses HL7 or it's use. And HL7 may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.
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  • Mondo Disease Ontology: Bundle/PhenopacketsBundleExample01, Condition/CHF-stageIII and Condition/intellectualDisabilityDisease
• The HPO vocabularies, annotation files, tools and documentation are freely available.
• The HPO is copyrighted to protect the integrity of the vocabularies, which means that changes to the HPO vocabularies need to be done by HPO developers. However, anyone can download the HPO and use the ontologies or other HPO files under three conditions:
• That the Human Phenotype Ontology Consortium is acknowledged and cited properly.
• That any HPO Consortium file(s) displayed publicly include the date(s) and/or version number(s) of the relevant HPO file(s).
• That neither the content of the HPO file(s) nor the logical relationships embedded within the HPO file(s) be altered in any way. (Content additions and modifications have to be suggested using our issue tracker .)
• Users of the HPO should add the following statement to their online presence. This service/product uses the Human Phenotype Ontology (version information). Find out more at http://www.human-phenotype-ontology.org. We request that the HPO logo be included as well.
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• Human Phenotype Ontology: Bundle/PhenopacketsBundleExample01, CodedOnset... Show 23 more, HpoSeverityVS, Observation/CHF-with-severity, Observation/MVP-with-onset, Observation/Polydactyly-with-modifier, Observation/amyotrophy, Observation/arachnodactyly, Observation/globalDevelopmentalDelay, Observation/hp.0003557, Observation/hypotonia, Observation/longPhiltrum, Observation/lowSetEars, Observation/lvdysfunction-excluded, Observation/microphthalmia, Observation/muscleWeakness, Observation/phenotypic-abnormality-invalid-1, Observation/phenotypic-abnormality-valid-1, Observation/reducedVisualAcuity, Observation/retinalDetachment, Observation/tga, Onset, PhenotypicComponentValueSet, PhenotypicFeature and PhenotypicModifierValueSet
• The UCUM codes, UCUM table (regardless of format), and UCUM Specification are copyright 1999-2009, Regenstrief Institute, Inc. and the Unified Codes for Units of Measures (UCUM) Organization. All rights reserved. https://ucum.org/trac/wiki/TermsOfUse
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  • Unified Code for Units of Measure (UCUM): Bundle/PhenopacketsBundleExample01, MedicationAdministration/losartan and Observation/thrombocytopenia
• This material contains content from LOINC. LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc.
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  • LOINC: Bundle/PhenopacketsBundleExample01, Composition/DevelopmentalDelay... Show 21 more, Composition/PhenopacketCompositionExample01, Observation/CHF-with-severity, Observation/MVP-with-onset, Observation/PhenopacketsVariantExample01, Observation/Polydactyly-with-modifier, Observation/amyotrophy, Observation/arachnodactyly, Observation/globalDevelopmentalDelay, Observation/hp.0003557, Observation/hypotonia, Observation/longPhiltrum, Observation/lowSetEars, Observation/lvdysfunction-excluded, Observation/microphthalmia, Observation/muscleWeakness, Observation/reducedVisualAcuity, Observation/retinalDetachment, Observation/tga, Observation/thrombocytopenia, PhenopacketsVariant and PhenotypicFeatureStatusValueSet
• This material contains content that is copyright of SNOMED International. Implementers of these specifications must have the appropriate SNOMED CT Affiliate license - for more information contact https://www.snomed.org/get-snomed or info@snomed.org.
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  • SNOMED Clinical Terms® (SNOMED CT®): Bundle/PhenopacketsBundleExample01, CodedOnset... Show 6 more, Condition/CHF-stageIII, Condition/excluded-disease, Condition/vitreoretinochoroidopathy, DiagnosticReport/PhenopacketsGenomicInterpretationExample01, DiagnosticReport/PhenopacketsGenomicInterpretationExample02 and Onset