Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build 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 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.

Scope and Usage

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

Formal Views of Profile Content

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

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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

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

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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
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 | Specimen) Related identifiers or resources

doco 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 v7.3
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:

Maturity: 2

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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

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

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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
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 | Specimen) Related identifiers or resources

doco 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 v7.3
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:

Maturity: 2

 

Other representations of profile: CSV, Excel, Schematron