Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions
| Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file | Version: 4.0.0-cibuild | |||
| Standards status: Trial-use | Maturity Level: 2 | Computable Name: GenomicDataFile | ||
A profile of DocumentReference used to represent a genomics file.
The Genomic Data File profile is used to represent a genomic data file as a DocumentReference resource. It provides a standardized mechanism for communicating the availability of a file and the information required to retrieve and appropriately interpret its contents. This profile is intended for files that contain genomic data generated or used in the course of genomic testing, including, for example, sequence alignment files, variant call files, and other files supporting genomic analysis, interpretation, or reporting. The file itself may be made available through the DocumentReference.content.attachment element, using an accessible URL or other attachment representation as appropriate to the implementation.
This profile is used when genomic data must be exchanged, discovered, or referenced independently of a genomic report while retaining its relationship to the associated clinical and laboratory context. The DocumentReference.description element may be used to provide human-readable information about how the file was generated, such as the sequencing method, analysis pipeline, reference sequence build, or other relevant processing details. The profile may also reference related genomic report resources through DocumentReference.context.related, enabling consumers to associate the genomic data file with the report(s) for which it was generated, analyzed, or made available. The profile is not intended to encode the genomic observations or interpretations contained in the file; those data are represented using the applicable genomic reporting profiles or are retained in the referenced file.
The DocumentReference.context.related element may additionally be used to reference one or more related Specimen resources. This enables a direct, computable association between a genomic data file and the source specimen(s), or other specimens relevant to the generation or interpretation of the file. Referencing specimens in the document context supports traceability across the genomic testing workflow, including circumstances in which multiple specimens contribute to a file or when a file is derived from a specimen distinct from the specimen associated with a related genomic report.
Usages:
You can also check for usages in the FHIR IG Statistics
Description of Profiles, Differentials, Snapshots and how the different presentations work.
| Name | Flags | Card. | Type | Description & Constraints Filter:  |
|---|---|---|---|---|
  DocumentReference |
0..* | DocumentReference | A reference to a document | |
  implicitRules |
0..1 | uri | A set of rules under which this content was created | |
 modifierExtension |
0..* | Extension | Extensions that cannot be ignored | |
| status |
1..1 | code | current | superseded | entered-in-error Binding: DocumentReferenceStatus (required): The status of the document reference. | |
| description |
0..1 | string | Human-readable description to provide guidance on how the file was generated | |
  content |
1..* | BackboneElement | Document referenced | |
 modifierExtension |
0..* | Extension | Extensions that cannot be ignored even if unrecognized | |
 attachment |
1..1 | Attachment | Where to access the document | |
| Documentation for this format | ||||
| Path | Status | Usage | ValueSet | Version | Source |
| DocumentReference.status | Base | required | DocumentReferenceStatus | 📍4.0.1 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| dom-2 | error | DocumentReference | If the resource is contained in another resource, it SHALL NOT contain nested Resources |
contained.contained.empty()
|
| dom-3 | error | DocumentReference | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource |
contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
|
| dom-4 | error | DocumentReference | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated |
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
|
| dom-5 | error | DocumentReference | If a resource is contained in another resource, it SHALL NOT have a security label |
contained.meta.security.empty()
|
| dom-6 | best practice | DocumentReference | A resource should have narrative for robust management |
text.`div`.exists()
|
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both |
extension.exists() != value.exists()
|
This structure is derived from DocumentReference
| Name | Flags | Card. | Type | Description & Constraints Filter: |
|---|---|---|---|---|
| DocumentReference |
0..* | DocumentReference | A reference to a document | |
 description |
0..1 | string | Human-readable description to provide guidance on how the file was generated | |
| context |
||||
 related |
0..* | Reference(Genomic Report | Specimen) | Related identifiers or resources | |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints Filter: | ||||
|---|---|---|---|---|---|---|---|---|
| DocumentReference |
0..* | DocumentReference | A reference to a document | |||||
| id |
0..1 | id | Logical id of this artifact | |||||
| meta |
0..1 | Meta | Metadata about the resource | |||||
| implicitRules |
0..1 | uri | A set of rules under which this content was created | |||||
| language |
0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text |
0..1 | Narrative | Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements | |||||
| contained |
0..* | Resource | Contained, inline Resources | |||||
 extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
0..* | Extension | Extensions that cannot be ignored | |||||
| masterIdentifier |
0..1 | Identifier | Master Version Specific Identifier | |||||
| identifier |
0..* | Identifier | Other identifiers for the document | |||||
| status |
1..1 | code | current | superseded | entered-in-error Binding: DocumentReferenceStatus (required): The status of the document reference. | |||||
| docStatus |
0..1 | code | preliminary | final | amended | entered-in-error Binding: CompositionStatus (required): Status of the underlying document. | |||||
| type |
0..1 | CodeableConcept | Kind of document (LOINC if possible) Binding: DocumentTypeValueSet (preferred): Precise type of clinical document. | |||||
| category |
0..* | CodeableConcept | Categorization of document Binding: DocumentClassValueSet (example): High-level kind of a clinical document at a macro level. | |||||
| subject |
0..1 | Reference(Patient | Practitioner | Group | Device) | Who/what is the subject of the document | |||||
| date |
0..1 | instant | When this document reference was created | |||||
| author |
0..* | Reference(Practitioner | PractitionerRole | Organization | Device | Patient | RelatedPerson) | Who and/or what authored the document | |||||
| authenticator |
0..1 | Reference(Practitioner | PractitionerRole | Organization) | Who/what authenticated the document | |||||
| custodian |
0..1 | Reference(Organization) | Organization which maintains the document | |||||
 relatesTo |
0..* | BackboneElement | Relationships to other documents | |||||
 id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
0..* | Extension | Extensions that cannot be ignored even if unrecognized | |||||
| code |
1..1 | code | replaces | transforms | signs | appends Binding: DocumentRelationshipType (required): The type of relationship between documents. | |||||
| target |
1..1 | Reference(DocumentReference) | Target of the relationship | |||||
| description |
0..1 | string | Human-readable description to provide guidance on how the file was generated | |||||
| securityLabel |
0..* | CodeableConcept | Document security-tags Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System. | |||||
| content |
1..* | BackboneElement | Document referenced | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
0..* | Extension | Extensions that cannot be ignored even if unrecognized | |||||
| attachment |
1..1 | Attachment | Where to access the document | |||||
| format |
0..1 | Coding | Format/content rules for the document Binding: DocumentReferenceFormatCodeSet (preferred): Document Format Codes. | |||||
| context |
0..1 | BackboneElement | Clinical context of document | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
0..* | Extension | Extensions that cannot be ignored even if unrecognized | |||||
| encounter |
0..* | Reference(Encounter | EpisodeOfCare) | Context of the document content | |||||
| event |
0..* | CodeableConcept | Main clinical acts documented Binding: v3 Code System ActCode (example): This list of codes represents the main clinical acts being documented. | |||||
| period |
0..1 | Period | Time of service that is being documented | |||||
| facilityType |
0..1 | CodeableConcept | Kind of facility where patient was seen Binding: FacilityTypeCodeValueSet (example): XDS Facility Type. | |||||
| practiceSetting |
0..1 | CodeableConcept | Additional details about where the content was created (e.g. clinical specialty) Binding: PracticeSettingCodeValueSet (example): Additional details about where the content was created (e.g. clinical specialty). | |||||
| sourcePatientInfo |
0..1 | Reference(Patient) | Patient demographics from source | |||||
| related |
0..* | Reference(Genomic Report | Specimen) | Related identifiers or resources | |||||
| Documentation for this format | ||||||||
| Path | Status | Usage | ValueSet | Version | Source |
| DocumentReference.language | Base | preferred | Common Languages | 📍4.0.1 | FHIR Std. |
| DocumentReference.status | Base | required | DocumentReferenceStatus | 📍4.0.1 | FHIR Std. |
| DocumentReference.docStatus | Base | required | CompositionStatus | 📍4.0.1 | FHIR Std. |
| DocumentReference.type | Base | preferred | Document Type Value Set | 📍4.0.1 | FHIR Std. |
| DocumentReference.category | Base | example | Document Class Value Set | 📍4.0.1 | FHIR Std. |
| DocumentReference.relatesTo.code | Base | required | DocumentRelationshipType | 📍4.0.1 | FHIR Std. |
| DocumentReference.securityLabel | Base | extensible | SecurityLabels | 📍4.0.1 | FHIR Std. |
| DocumentReference.content.format | Base | preferred | DocumentReference Format Code Set | 📍4.0.1 | FHIR Std. |
| DocumentReference.context.event | Base | example | v3 Code System ActCode | 📦3.0.0 | THO v7.5 |
| DocumentReference.context.facilityType | Base | example | Facility Type Code Value Set | 📍4.0.1 | FHIR Std. |
| DocumentReference.context.practiceSetting | Base | example | Practice Setting Code Value Set | 📍4.0.1 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| dom-2 | error | DocumentReference | If the resource is contained in another resource, it SHALL NOT contain nested Resources |
contained.contained.empty()
|
| dom-3 | error | DocumentReference | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource |
contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
|
| dom-4 | error | DocumentReference | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated |
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
|
| dom-5 | error | DocumentReference | If a resource is contained in another resource, it SHALL NOT have a security label |
contained.meta.security.empty()
|
| dom-6 | best practice | DocumentReference | A resource should have narrative for robust management |
text.`div`.exists()
|
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both |
extension.exists() != value.exists()
|
This structure is derived from DocumentReference
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints Filter: |
|---|---|---|---|---|
| DocumentReference |
0..* | DocumentReference | A reference to a document | |
| implicitRules |
0..1 | uri | A set of rules under which this content was created | |
| modifierExtension |
0..* | Extension | Extensions that cannot be ignored | |
| status |
1..1 | code | current | superseded | entered-in-error Binding: DocumentReferenceStatus (required): The status of the document reference. | |
| description |
0..1 | string | Human-readable description to provide guidance on how the file was generated | |
| content |
1..* | BackboneElement | Document referenced | |
| modifierExtension |
0..* | Extension | Extensions that cannot be ignored even if unrecognized | |
| attachment |
1..1 | Attachment | Where to access the document | |
| Documentation for this format | ||||
| Path | Status | Usage | ValueSet | Version | Source |
| DocumentReference.status | Base | required | DocumentReferenceStatus | 📍4.0.1 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| dom-2 | error | DocumentReference | If the resource is contained in another resource, it SHALL NOT contain nested Resources |
contained.contained.empty()
|
| dom-3 | error | DocumentReference | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource |
contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
|
| dom-4 | error | DocumentReference | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated |
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
|
| dom-5 | error | DocumentReference | If a resource is contained in another resource, it SHALL NOT have a security label |
contained.meta.security.empty()
|
| dom-6 | best practice | DocumentReference | A resource should have narrative for robust management |
text.`div`.exists()
|
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both |
extension.exists() != value.exists()
|
Differential View
This structure is derived from DocumentReference
| Name | Flags | Card. | Type | Description & Constraints Filter: |
|---|---|---|---|---|
| DocumentReference |
0..* | DocumentReference | A reference to a document | |
| description |
0..1 | string | Human-readable description to provide guidance on how the file was generated | |
| context |
||||
| related |
0..* | Reference(Genomic Report | Specimen) | Related identifiers or resources | |
| Documentation for this format | ||||
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints Filter: | ||||
|---|---|---|---|---|---|---|---|---|
| DocumentReference |
0..* | DocumentReference | A reference to a document | |||||
| id |
0..1 | id | Logical id of this artifact | |||||
| meta |
0..1 | Meta | Metadata about the resource | |||||
| implicitRules |
0..1 | uri | A set of rules under which this content was created | |||||
| language |
0..1 | code | Language of the resource content Binding: CommonLanguages (preferred): A human language.
| |||||
| text |
0..1 | Narrative | Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements | |||||
| contained |
0..* | Resource | Contained, inline Resources | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
0..* | Extension | Extensions that cannot be ignored | |||||
| masterIdentifier |
0..1 | Identifier | Master Version Specific Identifier | |||||
| identifier |
0..* | Identifier | Other identifiers for the document | |||||
| status |
1..1 | code | current | superseded | entered-in-error Binding: DocumentReferenceStatus (required): The status of the document reference. | |||||
| docStatus |
0..1 | code | preliminary | final | amended | entered-in-error Binding: CompositionStatus (required): Status of the underlying document. | |||||
| type |
0..1 | CodeableConcept | Kind of document (LOINC if possible) Binding: DocumentTypeValueSet (preferred): Precise type of clinical document. | |||||
| category |
0..* | CodeableConcept | Categorization of document Binding: DocumentClassValueSet (example): High-level kind of a clinical document at a macro level. | |||||
| subject |
0..1 | Reference(Patient | Practitioner | Group | Device) | Who/what is the subject of the document | |||||
| date |
0..1 | instant | When this document reference was created | |||||
| author |
0..* | Reference(Practitioner | PractitionerRole | Organization | Device | Patient | RelatedPerson) | Who and/or what authored the document | |||||
| authenticator |
0..1 | Reference(Practitioner | PractitionerRole | Organization) | Who/what authenticated the document | |||||
| custodian |
0..1 | Reference(Organization) | Organization which maintains the document | |||||
| relatesTo |
0..* | BackboneElement | Relationships to other documents | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
0..* | Extension | Extensions that cannot be ignored even if unrecognized | |||||
| code |
1..1 | code | replaces | transforms | signs | appends Binding: DocumentRelationshipType (required): The type of relationship between documents. | |||||
| target |
1..1 | Reference(DocumentReference) | Target of the relationship | |||||
| description |
0..1 | string | Human-readable description to provide guidance on how the file was generated | |||||
| securityLabel |
0..* | CodeableConcept | Document security-tags Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System. | |||||
| content |
1..* | BackboneElement | Document referenced | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
0..* | Extension | Extensions that cannot be ignored even if unrecognized | |||||
| attachment |
1..1 | Attachment | Where to access the document | |||||
| format |
0..1 | Coding | Format/content rules for the document Binding: DocumentReferenceFormatCodeSet (preferred): Document Format Codes. | |||||
| context |
0..1 | BackboneElement | Clinical context of document | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
0..* | Extension | Extensions that cannot be ignored even if unrecognized | |||||
| encounter |
0..* | Reference(Encounter | EpisodeOfCare) | Context of the document content | |||||
| event |
0..* | CodeableConcept | Main clinical acts documented Binding: v3 Code System ActCode (example): This list of codes represents the main clinical acts being documented. | |||||
| period |
0..1 | Period | Time of service that is being documented | |||||
| facilityType |
0..1 | CodeableConcept | Kind of facility where patient was seen Binding: FacilityTypeCodeValueSet (example): XDS Facility Type. | |||||
| practiceSetting |
0..1 | CodeableConcept | Additional details about where the content was created (e.g. clinical specialty) Binding: PracticeSettingCodeValueSet (example): Additional details about where the content was created (e.g. clinical specialty). | |||||
| sourcePatientInfo |
0..1 | Reference(Patient) | Patient demographics from source | |||||
| related |
0..* | Reference(Genomic Report | Specimen) | Related identifiers or resources | |||||
| Documentation for this format | ||||||||
| Path | Status | Usage | ValueSet | Version | Source |
| DocumentReference.language | Base | preferred | Common Languages | 📍4.0.1 | FHIR Std. |
| DocumentReference.status | Base | required | DocumentReferenceStatus | 📍4.0.1 | FHIR Std. |
| DocumentReference.docStatus | Base | required | CompositionStatus | 📍4.0.1 | FHIR Std. |
| DocumentReference.type | Base | preferred | Document Type Value Set | 📍4.0.1 | FHIR Std. |
| DocumentReference.category | Base | example | Document Class Value Set | 📍4.0.1 | FHIR Std. |
| DocumentReference.relatesTo.code | Base | required | DocumentRelationshipType | 📍4.0.1 | FHIR Std. |
| DocumentReference.securityLabel | Base | extensible | SecurityLabels | 📍4.0.1 | FHIR Std. |
| DocumentReference.content.format | Base | preferred | DocumentReference Format Code Set | 📍4.0.1 | FHIR Std. |
| DocumentReference.context.event | Base | example | v3 Code System ActCode | 📦3.0.0 | THO v7.5 |
| DocumentReference.context.facilityType | Base | example | Facility Type Code Value Set | 📍4.0.1 | FHIR Std. |
| DocumentReference.context.practiceSetting | Base | example | Practice Setting Code Value Set | 📍4.0.1 | FHIR Std. |
| Id | Grade | Path(s) | Description | Expression |
| dom-2 | error | DocumentReference | If the resource is contained in another resource, it SHALL NOT contain nested Resources |
contained.contained.empty()
|
| dom-3 | error | DocumentReference | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource |
contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
|
| dom-4 | error | DocumentReference | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated |
contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
|
| dom-5 | error | DocumentReference | If a resource is contained in another resource, it SHALL NOT have a security label |
contained.meta.security.empty()
|
| dom-6 | best practice | DocumentReference | A resource should have narrative for robust management |
text.`div`.exists()
|
| ele-1 | error | **ALL** elements | All FHIR elements must have a @value or children |
hasValue() or (children().count() > id.count())
|
| ext-1 | error | **ALL** extensions | Must have either extensions or value[x], not both |
extension.exists() != value.exists()
|
This structure is derived from DocumentReference
Other representations of profile: CSV, Excel, Schematron
IG © 2025+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-cibuild based on FHIR 4.0.1. Generated 2026-11-02
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