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

## Resource Profile: Genomic Data File

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.

Usages:

- Refer to this Profile: Genomic Study Analysis Input, Genomic Study Analysis Output and Genomic Study Analysis Regions
- Examples for this Profile: DocumentReference/CNVAnalysis-called, DocumentReference/FullGenome-GRCh38, DocumentReference/SimpleVariantAnalysis-called, DocumentReference/UncallableRegions... Show 9 more, DocumentReference/WES-FullSequencedRegion-GRCh38, DocumentReference/WES-UncallableRegions-GRCh38, DocumentReference/genomicFileFatherBAM, DocumentReference/genomicFileMotherBAM, DocumentReference/genomicFileProbandBAM, DocumentReference/genomicFileProbandVCF, DocumentReference/genomicVCFfile-cnv, DocumentReference/genomicVCFfile-simple and DocumentReference/somaticVCFfile

You can also check for usages in the FHIR IG Statistics

### Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

- Key Elements Table
- Differential Table
- Snapshot Table
- Statistics/References
- All

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
DocumentReference |  | 0..* | DocumentReference | A reference to a document
implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored
status | ?!Σ | 1..1 | code | current | superseded | entered-in-error Binding: DocumentReferenceStatus (required): The status of the document reference.
description | Σ | 0..1 | string | Human-readable description to provide guidance on how the file was generated
content | Σ | 1..* | BackboneElement | Document referenced
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
attachment | Σ | 1..1 | Attachment | Where to access the document
Documentation for this format

#### Terminology Bindings

Path | Status | Usage | ValueSet | Version | Source
DocumentReference.status | Base | required | DocumentReferenceStatus | 📍4.0.1 | FHIR Std.

#### Constraints

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: Bindings Constraints Obligations
--- | --- | --- | --- | ---
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) | Related identifiers or resources
Documentation for this format

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
DocumentReference |  | 0..* | DocumentReference | A reference to a document
id | Σ | 0..1 | id | Logical id of this artifact
meta | Σ | 0..1 | Meta | Metadata about the resource
implicitRules | ?!Σ | 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.
Additional Bindings | Purpose
AllLanguages | Max Binding
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 | Σ | 0..1 | Identifier | Master Version Specific Identifier
identifier | Σ | 0..* | Identifier | Other identifiers for the document
status | ?!Σ | 1..1 | code | current | superseded | entered-in-error Binding: DocumentReferenceStatus (required): The status of the document reference.
docStatus | Σ | 0..1 | code | preliminary | final | amended | entered-in-error Binding: CompositionStatus (required): Status of the underlying document.
type | Σ | 0..1 | CodeableConcept | Kind of document (LOINC if possible) Binding: DocumentTypeValueSet (preferred): Precise type of clinical document.
category | Σ | 0..* | CodeableConcept | Categorization of document Binding: DocumentClassValueSet (example): High-level kind of a clinical document at a macro level.
subject | Σ | 0..1 | Reference(Patient | Practitioner | Group | Device) | Who/what is the subject of the document
date | Σ | 0..1 | instant | When this document reference was created
author | Σ | 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 | Σ | 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 | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | code | replaces | transforms | signs | appends Binding: DocumentRelationshipType (required): The type of relationship between documents.
target | Σ | 1..1 | Reference(DocumentReference) | Target of the relationship
description | Σ | 0..1 | string | Human-readable description to provide guidance on how the file was generated
securityLabel | Σ | 0..* | CodeableConcept | Document security-tags Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System.
content | Σ | 1..* | BackboneElement | Document referenced
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
attachment | Σ | 1..1 | Attachment | Where to access the document
format | Σ | 0..1 | Coding | Format/content rules for the document Binding: DocumentReferenceFormatCodeSet (preferred): Document Format Codes.
context | Σ | 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 | ?!Σ | 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 | Σ | 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) | Related identifiers or resources
Documentation for this format

#### Terminology Bindings

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 v6.5
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.

#### Constraints

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

Summary

Structures

This structure refers to these other structures:

- Genomic Report (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report)

Maturity: 2

Key Elements View

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
DocumentReference |  | 0..* | DocumentReference | A reference to a document
implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created
modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored
status | ?!Σ | 1..1 | code | current | superseded | entered-in-error Binding: DocumentReferenceStatus (required): The status of the document reference.
description | Σ | 0..1 | string | Human-readable description to provide guidance on how the file was generated
content | Σ | 1..* | BackboneElement | Document referenced
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
attachment | Σ | 1..1 | Attachment | Where to access the document
Documentation for this format

#### Terminology Bindings

Path | Status | Usage | ValueSet | Version | Source
DocumentReference.status | Base | required | DocumentReferenceStatus | 📍4.0.1 | FHIR Std.

#### Constraints

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: Bindings Constraints Obligations
--- | --- | --- | --- | ---
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) | Related identifiers or resources
Documentation for this format

Snapshot View

Name | Flags | Card. | Type | Description & Constraints Filter: Bindings Constraints Obligations
--- | --- | --- | --- | ---
DocumentReference |  | 0..* | DocumentReference | A reference to a document
id | Σ | 0..1 | id | Logical id of this artifact
meta | Σ | 0..1 | Meta | Metadata about the resource
implicitRules | ?!Σ | 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.
Additional Bindings | Purpose
AllLanguages | Max Binding
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 | Σ | 0..1 | Identifier | Master Version Specific Identifier
identifier | Σ | 0..* | Identifier | Other identifiers for the document
status | ?!Σ | 1..1 | code | current | superseded | entered-in-error Binding: DocumentReferenceStatus (required): The status of the document reference.
docStatus | Σ | 0..1 | code | preliminary | final | amended | entered-in-error Binding: CompositionStatus (required): Status of the underlying document.
type | Σ | 0..1 | CodeableConcept | Kind of document (LOINC if possible) Binding: DocumentTypeValueSet (preferred): Precise type of clinical document.
category | Σ | 0..* | CodeableConcept | Categorization of document Binding: DocumentClassValueSet (example): High-level kind of a clinical document at a macro level.
subject | Σ | 0..1 | Reference(Patient | Practitioner | Group | Device) | Who/what is the subject of the document
date | Σ | 0..1 | instant | When this document reference was created
author | Σ | 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 | Σ | 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 | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
code | Σ | 1..1 | code | replaces | transforms | signs | appends Binding: DocumentRelationshipType (required): The type of relationship between documents.
target | Σ | 1..1 | Reference(DocumentReference) | Target of the relationship
description | Σ | 0..1 | string | Human-readable description to provide guidance on how the file was generated
securityLabel | Σ | 0..* | CodeableConcept | Document security-tags Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System.
content | Σ | 1..* | BackboneElement | Document referenced
id |  | 0..1 | string | Unique id for inter-element referencing
extension |  | 0..* | Extension | Additional content defined by implementations
modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized
attachment | Σ | 1..1 | Attachment | Where to access the document
format | Σ | 0..1 | Coding | Format/content rules for the document Binding: DocumentReferenceFormatCodeSet (preferred): Document Format Codes.
context | Σ | 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 | ?!Σ | 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 | Σ | 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) | Related identifiers or resources
Documentation for this format

#### Terminology Bindings

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 v6.5
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.

#### Constraints

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

Summary

Structures

This structure refers to these other structures:

- Genomic Report (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report)

Maturity: 2

Other representations of profile: CSV, Excel, Schematron