Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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: 3.0.1-SNAPSHOT
Active as of 2024-07-15 Computable Name: GenomicDataFile

A profile of DocumentReference used to represent a genomics file.

Usage:

Formal Views of Profile Content

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

This structure is derived from DocumentReference

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. 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 status ?!Σ 1..1 code current | superseded | entered-in-error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.

... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
DocumentReference.statusrequiredDocumentReferenceStatus
http://hl7.org/fhir/ValueSet/document-reference-status|4.0.1
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorDocumentReferenceIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorDocumentReferenceIf 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-4errorDocumentReferenceIf 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-5errorDocumentReferenceIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceDocumentReferenceA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
NameFlagsCard.TypeDescription & Constraintsdoco
.. 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
... text 0..1 Narrative Text summary of the resource, for human interpretation
... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
DocumentReference.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
DocumentReference.statusrequiredDocumentReferenceStatus
http://hl7.org/fhir/ValueSet/document-reference-status|4.0.1
from the FHIR Standard
DocumentReference.docStatusrequiredCompositionStatus
http://hl7.org/fhir/ValueSet/composition-status|4.0.1
from the FHIR Standard
DocumentReference.typepreferredDocumentTypeValueSet
http://hl7.org/fhir/ValueSet/c80-doc-typecodes
from the FHIR Standard
DocumentReference.categoryexampleDocumentClassValueSet
http://hl7.org/fhir/ValueSet/document-classcodes
from the FHIR Standard
DocumentReference.relatesTo.coderequiredDocumentRelationshipType
http://hl7.org/fhir/ValueSet/document-relationship-type|4.0.1
from the FHIR Standard
DocumentReference.securityLabelextensibleAll Security Labels
http://hl7.org/fhir/ValueSet/security-labels
from the FHIR Standard
DocumentReference.content.formatpreferredDocumentReferenceFormatCodeSet (a valid code from http://ihe.net/fhir/ValueSet/IHE.FormatCode.codesystem)
http://hl7.org/fhir/ValueSet/formatcodes
from the FHIR Standard
DocumentReference.context.eventexampleActCode
http://terminology.hl7.org/ValueSet/v3-ActCode
DocumentReference.context.facilityTypeexampleFacilityTypeCodeValueSet
http://hl7.org/fhir/ValueSet/c80-facilitycodes
from the FHIR Standard
DocumentReference.context.practiceSettingexamplePracticeSettingCodeValueSet
http://hl7.org/fhir/ValueSet/c80-practice-codes
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorDocumentReferenceIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorDocumentReferenceIf 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-4errorDocumentReferenceIf 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-5errorDocumentReferenceIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceDocumentReferenceA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust 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:

Differential View

This structure is derived from DocumentReference

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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

doco Documentation for this format

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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.

... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
DocumentReference.statusrequiredDocumentReferenceStatus
http://hl7.org/fhir/ValueSet/document-reference-status|4.0.1
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorDocumentReferenceIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorDocumentReferenceIf 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-4errorDocumentReferenceIf 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-5errorDocumentReferenceIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceDocumentReferenceA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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
... text 0..1 Narrative Text summary of the resource, for human interpretation
... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
DocumentReference.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
DocumentReference.statusrequiredDocumentReferenceStatus
http://hl7.org/fhir/ValueSet/document-reference-status|4.0.1
from the FHIR Standard
DocumentReference.docStatusrequiredCompositionStatus
http://hl7.org/fhir/ValueSet/composition-status|4.0.1
from the FHIR Standard
DocumentReference.typepreferredDocumentTypeValueSet
http://hl7.org/fhir/ValueSet/c80-doc-typecodes
from the FHIR Standard
DocumentReference.categoryexampleDocumentClassValueSet
http://hl7.org/fhir/ValueSet/document-classcodes
from the FHIR Standard
DocumentReference.relatesTo.coderequiredDocumentRelationshipType
http://hl7.org/fhir/ValueSet/document-relationship-type|4.0.1
from the FHIR Standard
DocumentReference.securityLabelextensibleAll Security Labels
http://hl7.org/fhir/ValueSet/security-labels
from the FHIR Standard
DocumentReference.content.formatpreferredDocumentReferenceFormatCodeSet (a valid code from http://ihe.net/fhir/ValueSet/IHE.FormatCode.codesystem)
http://hl7.org/fhir/ValueSet/formatcodes
from the FHIR Standard
DocumentReference.context.eventexampleActCode
http://terminology.hl7.org/ValueSet/v3-ActCode
DocumentReference.context.facilityTypeexampleFacilityTypeCodeValueSet
http://hl7.org/fhir/ValueSet/c80-facilitycodes
from the FHIR Standard
DocumentReference.context.practiceSettingexamplePracticeSettingCodeValueSet
http://hl7.org/fhir/ValueSet/c80-practice-codes
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorDocumentReferenceIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorDocumentReferenceIf 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-4errorDocumentReferenceIf 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-5errorDocumentReferenceIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceDocumentReferenceA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust 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:

 

Other representations of profile: CSV, Excel, Schematron