Genomics Reporting Implementation Guide
2.0.0 - trial-use
Genomics Reporting Implementation Guide
2.0.0 - trial-use
This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions 
| Defining URL: | http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-document-reference |
| Version: | 2.0.0 |
| Name: | GenomicsDocumentReference |
| Title: | Genomics DocumentReference |
| Status: | Active as of 2022-05-09 04:53:07+0000 |
| Definition: | A profile of DocumentReference used to represent a genomics file. |
| Publisher: | HL7 Clinical Genomics Working Group |
| Source Resource: | XML / JSON / Turtle |
The official URL for this profile is:
http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-document-reference
This approach to file attachments needs to be carefully reviewed and considered. There are many potential issues and the Work Group welcomes feedback.
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from DocumentReference
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(Genomics Report) | Related identifiers or resources | |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| DocumentReference | 0..* | DocumentReference | A reference to a document | |||||
 id | Σ | 0..1 | string | 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.
| |||||
| 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(Genomics Report) | Related identifiers or resources | |||||
| Documentation for this format | ||||||||
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| DocumentReference | 0..* | DocumentReference | A reference to a document | |
| Documentation for this format | ||||
This structure is derived from DocumentReference
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(Genomics Report) | Related identifiers or resources | |
| Documentation for this format | ||||
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints | ||||
|---|---|---|---|---|---|---|---|---|
| DocumentReference | 0..* | DocumentReference | A reference to a document | |||||
| id | Σ | 0..1 | string | 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.
| |||||
| 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(Genomics Report) | Related identifiers or resources | |||||
| Documentation for this format | ||||||||
Other representations of profile: CSV, Excel, Schematron
| Path | Conformance | ValueSet |
| DocumentReference.language | preferred | CommonLanguages Max Binding: AllLanguages |
| DocumentReference.status | required | DocumentReferenceStatus |
| DocumentReference.docStatus | required | CompositionStatus |
| DocumentReference.type | preferred | DocumentTypeValueSet |
| DocumentReference.category | example | DocumentClassValueSet |
| DocumentReference.relatesTo.code | required | DocumentRelationshipType |
| DocumentReference.securityLabel | extensible | All Security Labels |
| DocumentReference.content.format | preferred | DocumentReferenceFormatCodeSet |
| DocumentReference.context.event | example | ActCode |
| DocumentReference.context.facilityType | example | FacilityTypeCodeValueSet |
| DocumentReference.context.practiceSetting | example | PracticeSettingCodeValueSet |
| Id | Grade | Path | 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 | DocumentReference.meta | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.implicitRules | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.language | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.text | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.extension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | DocumentReference.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | error | DocumentReference.modifierExtension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | DocumentReference.modifierExtension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | error | DocumentReference.masterIdentifier | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.identifier | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.status | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.docStatus | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.type | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.category | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.subject | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.date | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.author | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.authenticator | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.custodian | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.relatesTo | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.relatesTo.extension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | DocumentReference.relatesTo.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | error | DocumentReference.relatesTo.modifierExtension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | DocumentReference.relatesTo.modifierExtension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | error | DocumentReference.relatesTo.code | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.relatesTo.target | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.description | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.securityLabel | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.content | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.content.extension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | DocumentReference.content.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | error | DocumentReference.content.modifierExtension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | DocumentReference.content.modifierExtension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | error | DocumentReference.content.attachment | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.content.format | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.context | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.context.extension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | DocumentReference.context.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | error | DocumentReference.context.modifierExtension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | error | DocumentReference.context.modifierExtension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | error | DocumentReference.context.encounter | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.context.event | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.context.period | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.context.facilityType | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.context.practiceSetting | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.context.sourcePatientInfo | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | error | DocumentReference.context.related | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) |
IG © 2022+ HL7 Clinical Genomics Working Group. Package hl7.fhir.uv.genomics-reporting#2.0.0 based on FHIR 4.0.1. Generated 2022-05-09
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