Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions
| Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file | Version: 3.0.0-ballot | |||
| Active as of 2023-12-18 | Computable Name: GenomicDataFile | |||
A profile of DocumentReference used to represent a genomics file.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
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| status | ?!Σ | 1..1 | code | current | superseded | entered-in-error Binding: DocumentReferenceStatus (required): The status of the document reference.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 | ||||
| Path | Conformance | ValueSet |
| DocumentReference.status | required | DocumentReferenceStatus |
| 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.
| |||||
| 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 | ||||||||
| Path | Conformance | ValueSet | ||||
| DocumentReference.language | preferred | CommonLanguages
| ||||
| 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 (a valid code from http://ihe.net/fhir/ValueSet/IHE.FormatCode.codesystem) | ||||
| DocumentReference.context.event | example | ActCode | ||||
| DocumentReference.context.facilityType | example | FacilityTypeCodeValueSet | ||||
| DocumentReference.context.practiceSetting | example | PracticeSettingCodeValueSet |
| 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
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 | ||||
| Path | Conformance | ValueSet |
| DocumentReference.status | required | DocumentReferenceStatus |
| 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.
| |||||
| 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 | ||||||||
| Path | Conformance | ValueSet | ||||
| DocumentReference.language | preferred | CommonLanguages
| ||||
| 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 (a valid code from http://ihe.net/fhir/ValueSet/IHE.FormatCode.codesystem) | ||||
| DocumentReference.context.event | example | ActCode | ||||
| DocumentReference.context.facilityType | example | FacilityTypeCodeValueSet | ||||
| DocumentReference.context.practiceSetting | example | PracticeSettingCodeValueSet |
| 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
Other representations of profile: CSV, Excel, Schematron
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0-ballot based on FHIR 4.0.1. Generated 2023-12-18
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