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

• Content
• Detailed Descriptions
• Mappings
• Examples
• XML
• JSON
• TTL

Resource Profile: Genomic Data File

A profile of DocumentReference used to represent a genomics file.

Usage:

• Refer to this Resource Profile: Genomic Study Analysis Input, Genomic Study Analysis Output and Genomic Study Analysis Regions
• Examples for this Resource 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

Formal Views of Profile Content

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

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

This structure is derived from DocumentReference

Name	Flags	Card.	Type	Description & Constraints
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
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status	?!Σ	1..1	code	current | superseded | entered-in-error Binding: DocumentReferenceStatus (required): The status of the document reference.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	Conformance	ValueSet	URI
DocumentReference.status	required	DocumentReferenceStatus http://hl7.org/fhir/ValueSet/document-reference-status|4.0.1 from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
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()

Name	Flags	Card.	Type	Description & Constraints
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
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	Conformance	ValueSet	URI
DocumentReference.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding http://hl7.org/fhir/ValueSet/languages from the FHIR Standard
DocumentReference.status	required	DocumentReferenceStatus http://hl7.org/fhir/ValueSet/document-reference-status|4.0.1 from the FHIR Standard
DocumentReference.docStatus	required	CompositionStatus http://hl7.org/fhir/ValueSet/composition-status|4.0.1 from the FHIR Standard
DocumentReference.type	preferred	DocumentTypeValueSet http://hl7.org/fhir/ValueSet/c80-doc-typecodes from the FHIR Standard
DocumentReference.category	example	DocumentClassValueSet http://hl7.org/fhir/ValueSet/document-classcodes from the FHIR Standard
DocumentReference.relatesTo.code	required	DocumentRelationshipType http://hl7.org/fhir/ValueSet/document-relationship-type|4.0.1 from the FHIR Standard
DocumentReference.securityLabel	extensible	All Security Labels http://hl7.org/fhir/ValueSet/security-labels from the FHIR Standard
DocumentReference.content.format	preferred	DocumentReferenceFormatCodeSet (a valid code from http://ihe.net/fhir/ValueSet/IHE.FormatCode.codesystem) http://hl7.org/fhir/ValueSet/formatcodes from the FHIR Standard
DocumentReference.context.event	example	ActCode http://terminology.hl7.org/ValueSet/v3-ActCode
DocumentReference.context.facilityType	example	FacilityTypeCodeValueSet http://hl7.org/fhir/ValueSet/c80-facilitycodes from the FHIR Standard
DocumentReference.context.practiceSetting	example	PracticeSettingCodeValueSet http://hl7.org/fhir/ValueSet/c80-practice-codes from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
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)

Differential View

This structure is derived from DocumentReference

Name	Flags	Card.	Type	Description & Constraints
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

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
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	Conformance	ValueSet	URI
DocumentReference.status	required	DocumentReferenceStatus http://hl7.org/fhir/ValueSet/document-reference-status|4.0.1 from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
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()

Snapshot View

Name	Flags	Card.	Type	Description & Constraints
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
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	Conformance	ValueSet	URI
DocumentReference.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding http://hl7.org/fhir/ValueSet/languages from the FHIR Standard
DocumentReference.status	required	DocumentReferenceStatus http://hl7.org/fhir/ValueSet/document-reference-status|4.0.1 from the FHIR Standard
DocumentReference.docStatus	required	CompositionStatus http://hl7.org/fhir/ValueSet/composition-status|4.0.1 from the FHIR Standard
DocumentReference.type	preferred	DocumentTypeValueSet http://hl7.org/fhir/ValueSet/c80-doc-typecodes from the FHIR Standard
DocumentReference.category	example	DocumentClassValueSet http://hl7.org/fhir/ValueSet/document-classcodes from the FHIR Standard
DocumentReference.relatesTo.code	required	DocumentRelationshipType http://hl7.org/fhir/ValueSet/document-relationship-type|4.0.1 from the FHIR Standard
DocumentReference.securityLabel	extensible	All Security Labels http://hl7.org/fhir/ValueSet/security-labels from the FHIR Standard
DocumentReference.content.format	preferred	DocumentReferenceFormatCodeSet (a valid code from http://ihe.net/fhir/ValueSet/IHE.FormatCode.codesystem) http://hl7.org/fhir/ValueSet/formatcodes from the FHIR Standard
DocumentReference.context.event	example	ActCode http://terminology.hl7.org/ValueSet/v3-ActCode
DocumentReference.context.facilityType	example	FacilityTypeCodeValueSet http://hl7.org/fhir/ValueSet/c80-facilitycodes from the FHIR Standard
DocumentReference.context.practiceSetting	example	PracticeSettingCodeValueSet http://hl7.org/fhir/ValueSet/c80-practice-codes from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
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)

Other representations of profile: CSV, Excel, Schematron