Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions
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Overview
The Clinical Genomics Incubator Implementation Guide defines foundational resources for genomic data exchange and analysis. This IG serves as an incubator for Clinical Genomics Work Group, hosting additional resources designed to be leveraged by other implementation guides such as Genomics Reporting and Molecular Definition Data Types.
Primary Resources
This IG defines two additional resources:
GenomicStudy
GenomicStudy represents a set of analyses performed to analyze and generate genomic data. This resource captures the overall genomic testing event, including information about the type of study, the subject being studied, associated test results, and metadata about the genomic analysis performed. It serves as the umbrella resource for organizing and tracking genomic studies within clinical workflows.
MolecularDefinition
MolecularDefinition provides definitional content for molecular entities, such as nucleotide or protein sequences. This resource enables precise representation of molecular components referenced in genomic studies, including structural information about molecules and their compositions. It serves as a foundational building block for representing complex molecular data.
About Additional Resources
This implementation guide publishes Additional Resources, which are FHIR resources that go beyond the base FHIR specification. These resources are designed to meet specific clinical and technical needs while undergoing development and refinement. Additional Resources allow implementers to use these specialized resources in production implementations while the resources continue to evolve through the standards development process.
The resources defined in this IG are intended to be integrated into the base FHIR specification once they have matured through community feedback and validation in real-world implementations.
Cross Version Analysis
Dependency Table
Package hl7.fhir.uv.extensions.r5#5.2.0
This IG defines the global extensions - the ones defined for everyone. These extensions are always in scope wherever FHIR is being used (built Mon, Feb 10, 2025 21:45+1100+11:00)
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Package hl7.fhir.uv.tools.r5#1.1.0
This IG defines the extensions that the tools use internally. Some of these extensions are content that are being evaluated for elevation into the main spec, and others are tooling concerns (built Tue, Mar 3, 2026 22:50+1100+11:00)
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Global Profiles Table
There are no Global profiles defined
IP Statements
This publication includes IP covered under the following statements.
- NCBI Taxonomy data is a product of the National Center for Biotechnology Information (NCBI), part of the National Library of Medicine at the National Institutes of Health. The database is freely available in the public domain.
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- 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: GenomicStudy/example, GenomicStudy/example-lungMass... Show 40 more, GenomicStudy/example-pgx, GenomicStudy/example-somaticStudy, GenomicStudy/example-trio2, MolecularDefinition/example, MolecularDefinition/example-allele1, MolecularDefinition/example-allele2, MolecularDefinition/example-allele3, MolecularDefinition/example-allele4, MolecularDefinition/example-allele5, MolecularDefinition/example-allele6, MolecularDefinition/example-allele7, MolecularDefinition/example-allelesliced-cyp2c19-1016, MolecularDefinition/example-allelesliced-cyp2c19-661, MolecularDefinition/example-allelesliced-cyp2c19-literal-only, MolecularDefinition/example-allelesliced-hla00381, MolecularDefinition/example-allelesliced-pgx-var-1011, MolecularDefinition/example-allelesliced1, MolecularDefinition/example-haplotype1, MolecularDefinition/example-sequence-cyp2c19-downstream-region, MolecularDefinition/example-sequence-cyp2c19-gene-region, MolecularDefinition/example-sequence-cyp2c19-upstream-region, MolecularDefinition/example-sequence-fmr1-cgg-20x-edited-referenced, MolecularDefinition/example-sequence1, MolecularDefinition/example-variation-cyp2c19-1015-spdi, MolecularDefinition/example-variation-cyp2c19-1015-vrs, MolecularDefinition/example-variation-cyp2c19-1016-vcf, MolecularDefinition/example-variation-cyp2c19-661, MolecularDefinition/example-variation-cyp2c19-991-hgvs, MolecularDefinition/example-variation-pgx-var-1011, MolecularDefinition/example-variation-pgx-var-1012, MolecularDefinition/example-variation-pgx-var-1013, MolecularDefinition/example-variation-pgx-var-1014, MolecularDefinition/example-variation-pgx-var-1015, MolecularDefinition/example-variation-pgx-var-1016, MolecularDefinition/example-variation-pgx-var-1017, MolecularDefinition/example-variation-pgx-var-1018, MolecularDefinition/example-variation-pgx-var-1019, MolecularDefinition/example-variation-pgx-var-1020, MolecularDefinition/example-variation-pgx-var-1021 and MolecularDefinition/example-variation1
- 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®): Device/NGS-device, Device/Triodenovo-SW... Show 24 more, GenomicStudy/example, GenomicStudy/example-lungMass, GenomicStudy/example-pgx, GenomicStudy/example-somaticStudy, GenomicStudy/example-trio2, ServiceRequest/genomicSRFather, ServiceRequest/genomicSRMother, ServiceRequest/genomicSRProband, ServiceRequest/genomicServiceRequest, ServiceRequest/genomicServiceRequest2, ServiceRequest/genomicServiceRequest3, ServiceRequest/genomicServiceRequest4, ServiceRequest/pgxServiceRequest, ServiceRequest/somaticServiceRequest, Specimen/denovo-1, Specimen/denovo-2, Specimen/denovo-3, Specimen/genomicSpecimen, Specimen/normalSpecimen, Specimen/pgxSpecimen, Specimen/specimenFather, Specimen/specimenMother, Specimen/specimenProband and Specimen/tumorSpecimen
- This material derives from the HL7 Terminology (THO). THO is copyright ©1989+ Health Level Seven International and is made available under the CC0 designation. For more licensing information see: https://terminology.hl7.org/license.html
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- identifierType: Denovo Mutation Example Group, Patient/denovoChild... Show 19 more, Patient/denovoFather, Patient/denovoMother, Patient/father, Patient/genomicPatient, Patient/mother, Patient/pgxPatient, Patient/proband, Patient/somaticPatient, Practitioner/practitioner01, Practitioner/practitioner02, RelatedPerson/relatedPersonDenovoFather, RelatedPerson/relatedPersonDenovoMother, ServiceRequest/genomicSRFather, ServiceRequest/genomicSRMother, ServiceRequest/genomicSRProband, ServiceRequest/genomicServiceRequest, ServiceRequest/genomicServiceRequest2, ServiceRequest/genomicServiceRequest3 and ServiceRequest/genomicServiceRequest4
- specimenCollectionMethod: Specimen/denovo-1, Specimen/denovo-2... Show 4 more, Specimen/denovo-3, Specimen/specimenFather, Specimen/specimenMother and Specimen/specimenProband
- ActCode: Encounter/denovoEncounter and Encounter/genomicEncounter
- Confidentiality: DocumentReference/pgxVCFfile, DocumentReference/somaticCalledRegions, DocumentReference/somaticFusionFile, DocumentReference/somaticRNAstudiedRegions and DocumentReference/somaticVCFfile
- ParticipationType: GenomicStudy/example, GenomicStudy/example-lungMass, GenomicStudy/example-pgx, GenomicStudy/example-somaticStudy and GenomicStudy/example-trio2
- RoleCode: RelatedPerson/relatedPersonDenovoFather and RelatedPerson/relatedPersonDenovoMother