Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
| Defining URL: | http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report |
| Version: | 1.1.0 |
| Name: | GenomicsReport |
| Title: | Genomics Report |
| Status: | Active as of 2021-04-13T19:13:37+00:00 |
| Definition: | Genomics profile of DiagnosticReport. |
| Publisher: | HL7 International Clinical Genomics Work Group |
| Source Resource: | XML / JSON / Turtle |
The official URL for this profile is:
http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from DiagnosticReport
Summary
Mandatory: 3 elements
Prohibited: 1 element
Structures
This structure refers to these other structures:
Extensions
This structure refers to these extensions:
Slices
This structure defines the following Slices:
This structure is derived from DiagnosticReport
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  DiagnosticReport | 0..* | DiagnosticReport | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |
  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) Max Binding: AllLanguages: A human language. | |
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |
| contained | 0..* | Resource | Contained, inline Resources | |
 extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
 CGRelatedArtifact | 0..* | RelatedArtifact | Related Artifact URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/CGRelatedArtifact | |
 RecommendedAction | 0..* | Reference(Task | ServiceRequest | MedicationRequest | RequestGroup | CarePlan | DeviceRequest | NutritionOrder | SupplyRequest) | Recommended Action URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RecommendedAction | |
  id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..0 | |||
| url | 1..1 | uri | "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RecommendedAction" | |
  value[x] | 0..1 | Reference(Task) | Value of extension | |
| SupportingInfo | 0..* | Reference(Resource) | Supporting Information URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/SupportingInfo | |
| diagnosticReport-risk | 0..* | Reference(RiskAssessment) | Risk Assessment Reference URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnosticReport-risk | |
 modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| identifier | Σ | 0..* | Identifier | Business identifier for report |
| basedOn | 0..* | Reference(Genomics service request) | What was requested | |
| status | ?!Σ | 1..1 | code | registered | partial | preliminary | final + Binding: DiagnosticReportStatus (required): The status of the diagnostic report. |
 category | Σ | 1..* | (Slice Definition) | Service category Slice: Unordered, Open by pattern:coding Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. |
 category:Genetics | Σ | 1..1 | CodeableConcept | Service category Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. |
 id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |
 coding | Σ | 1..* | Coding | Code defined by a terminology system Required Pattern: At least the following |
 id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
 system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| display | 0..1 | string | Representation defined by the system | |
 userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | Σ | 0..1 | string | Plain text representation of the concept |
| code | Σ | 1..1 | CodeableConcept | Name/Code for this diagnostic report Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports. |
| subject | Σ | 0..1 | Reference(Patient | Group | Location) | The subject of the report - usually, but not always, the patient |
| encounter | Σ | 0..1 | Reference(Encounter) | Health care event when test ordered |
| effective[x] | Σ | 0..1 | dateTime | Clinically relevant time/time-period for report |
| issued | Σ | 0..1 | instant | DateTime this version was made |
| performer | Σ | 0..1 | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Responsible Diagnostic Service |
| resultsInterpreter | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Primary result interpreter |
| specimen | 0..* | Reference(Genomics specimen) | Specimens this report is based on | |
| result | 0..* | (Slice Definition) | Observations Slice: Unordered, Open by profile:resolve() | |
 result:gen-grouper | 0..* | Reference(Grouper) | Grouper | |
| result:overall | 0..1 | Reference(Overall Interpretation) | Assessment of overall results | |
| result:diagnostic-implication | 0..* | Reference(Diagnostic Implication) | Diagnostic Implication | |
| result:therapeutic-implication | 0..* | Reference(Therapeutic Implication) | Therapeutic Implication | |
| result:variant | 0..* | Reference(Variant) | Variant | |
| result:sequence-phase-relation | 0..* | Reference(Sequence Phase Relationship) | Sequence Phase Relationship | |
| result:region-studied | 0..* | Reference(Region Studied) | Region Studied | |
| result:genotype | 0..* | Reference(Genotype) | Genotype | |
 result:haplotype | 0..* | Reference(Haplotype) | Haplotype | |
| media | Σ | 0..1 | BackboneElement | Key images associated with this report |
| 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 |
| comment | 0..1 | string | Comment about the image (e.g. explanation) | |
| link | Σ | 1..1 | Reference(Media) | Reference to the image source |
| conclusion | 0..1 | string | Clinical conclusion (interpretation) of test results | |
| conclusionCode | 0..* | CodeableConcept | Codes for the clinical conclusion of test results Binding: SNOMEDCTClinicalFindings (example): Diagnosis codes provided as adjuncts to the report. | |
| presentedForm | 0..* | Attachment | Entire report as issued | |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| DiagnosticReport | 0..* | DiagnosticReport | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |
| Documentation for this format | ||||
This structure is derived from DiagnosticReport
Summary
Mandatory: 3 elements
Prohibited: 1 element
Structures
This structure refers to these other structures:
Extensions
This structure refers to these extensions:
Slices
This structure defines the following Slices:
Differential View
This structure is derived from DiagnosticReport
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| DiagnosticReport | 0..* | DiagnosticReport | A Diagnostic report - a combination of request information, atomic results, images, interpretation, as well as formatted reports | |
| 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) Max Binding: AllLanguages: A human language. | |
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |
| contained | 0..* | Resource | Contained, inline Resources | |
| extension | 0..* | Extension | Extension Slice: Unordered, Open by value:url | |
| CGRelatedArtifact | 0..* | RelatedArtifact | Related Artifact URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/CGRelatedArtifact | |
| RecommendedAction | 0..* | Reference(Task | ServiceRequest | MedicationRequest | RequestGroup | CarePlan | DeviceRequest | NutritionOrder | SupplyRequest) | Recommended Action URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RecommendedAction | |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..0 | |||
| url | 1..1 | uri | "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RecommendedAction" | |
| value[x] | 0..1 | Reference(Task) | Value of extension | |
| SupportingInfo | 0..* | Reference(Resource) | Supporting Information URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/SupportingInfo | |
| diagnosticReport-risk | 0..* | Reference(RiskAssessment) | Risk Assessment Reference URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/diagnosticReport-risk | |
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| identifier | Σ | 0..* | Identifier | Business identifier for report |
| basedOn | 0..* | Reference(Genomics service request) | What was requested | |
| status | ?!Σ | 1..1 | code | registered | partial | preliminary | final + Binding: DiagnosticReportStatus (required): The status of the diagnostic report. |
| category | Σ | 1..* | (Slice Definition) | Service category Slice: Unordered, Open by pattern:coding Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. |
| category:Genetics | Σ | 1..1 | CodeableConcept | Service category Binding: DiagnosticServiceSectionCodes (example): Codes for diagnostic service sections. |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |
| coding | Σ | 1..* | Coding | Code defined by a terminology system Required Pattern: At least the following |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| system | 1..1 | uri | Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074 | |
| version | 0..1 | string | Version of the system - if relevant | |
| code | 1..1 | code | Symbol in syntax defined by the system Fixed Value: GE | |
| display | 0..1 | string | Representation defined by the system | |
| userSelected | 0..1 | boolean | If this coding was chosen directly by the user | |
| text | Σ | 0..1 | string | Plain text representation of the concept |
| code | Σ | 1..1 | CodeableConcept | Name/Code for this diagnostic report Binding: LOINCDiagnosticReportCodes (preferred): Codes that describe Diagnostic Reports. |
| subject | Σ | 0..1 | Reference(Patient | Group | Location) | The subject of the report - usually, but not always, the patient |
| encounter | Σ | 0..1 | Reference(Encounter) | Health care event when test ordered |
| effective[x] | Σ | 0..1 | dateTime | Clinically relevant time/time-period for report |
| issued | Σ | 0..1 | instant | DateTime this version was made |
| performer | Σ | 0..1 | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Responsible Diagnostic Service |
| resultsInterpreter | Σ | 0..* | Reference(Practitioner | PractitionerRole | Organization | CareTeam) | Primary result interpreter |
| specimen | 0..* | Reference(Genomics specimen) | Specimens this report is based on | |
| result | 0..* | (Slice Definition) | Observations Slice: Unordered, Open by profile:resolve() | |
| result:gen-grouper | 0..* | Reference(Grouper) | Grouper | |
| result:overall | 0..1 | Reference(Overall Interpretation) | Assessment of overall results | |
| result:diagnostic-implication | 0..* | Reference(Diagnostic Implication) | Diagnostic Implication | |
| result:therapeutic-implication | 0..* | Reference(Therapeutic Implication) | Therapeutic Implication | |
| result:variant | 0..* | Reference(Variant) | Variant | |
| result:sequence-phase-relation | 0..* | Reference(Sequence Phase Relationship) | Sequence Phase Relationship | |
| result:region-studied | 0..* | Reference(Region Studied) | Region Studied | |
| result:genotype | 0..* | Reference(Genotype) | Genotype | |
| result:haplotype | 0..* | Reference(Haplotype) | Haplotype | |
| media | Σ | 0..1 | BackboneElement | Key images associated with this report |
| 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 |
| comment | 0..1 | string | Comment about the image (e.g. explanation) | |
| link | Σ | 1..1 | Reference(Media) | Reference to the image source |
| conclusion | 0..1 | string | Clinical conclusion (interpretation) of test results | |
| conclusionCode | 0..* | CodeableConcept | Codes for the clinical conclusion of test results Binding: SNOMEDCTClinicalFindings (example): Diagnosis codes provided as adjuncts to the report. | |
| presentedForm | 0..* | Attachment | Entire report as issued | |
| Documentation for this format | ||||
Other representations of profile: Schematron
| Path | Conformance | ValueSet |
| DiagnosticReport.language | preferred | CommonLanguages Max Binding: AllLanguages |
| DiagnosticReport.status | required | DiagnosticReportStatus |
| DiagnosticReport.category | example | DiagnosticServiceSectionCodes |
| DiagnosticReport.category:Genetics | example | DiagnosticServiceSectionCodes |
| DiagnosticReport.code | preferred | LOINCDiagnosticReportCodes |
| DiagnosticReport.conclusionCode | example | SNOMEDCTClinicalFindings |
| Id | Path | Details | Requirements |
| dom-2 | DiagnosticReport | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | DiagnosticReport | 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 | DiagnosticReport | 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 | DiagnosticReport | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | DiagnosticReport | A resource should have narrative for robust management : text.`div`.exists() | |
| ele-1 | DiagnosticReport.meta | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.implicitRules | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.language | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.text | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.extension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | DiagnosticReport.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | DiagnosticReport.extension:relatedArtifact | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | DiagnosticReport.extension:relatedArtifact | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | DiagnosticReport.extension:RecommendedAction | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | DiagnosticReport.extension:RecommendedAction | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | DiagnosticReport.extension:RecommendedAction.value[x] | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.extension:SupportingInfo | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | DiagnosticReport.extension:SupportingInfo | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | DiagnosticReport.extension:diagnosticReport-risk | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | DiagnosticReport.extension:diagnosticReport-risk | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | DiagnosticReport.modifierExtension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | DiagnosticReport.modifierExtension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | DiagnosticReport.identifier | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.basedOn | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.status | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.category | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.category:Genetics | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.category:Genetics.extension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | DiagnosticReport.category:Genetics.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | DiagnosticReport.category:Genetics.coding | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.category:Genetics.text | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.code | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.subject | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.encounter | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.effective[x] | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.issued | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.performer | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.resultsInterpreter | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.specimen | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.result | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.result:gen-grouper | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.result:overall | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.result:diagnostic-implication | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.result:therapeutic-implication | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.result:variant | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.result:sequence-phase-relation | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.result:region-studied | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.result:genotype | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.result:haplotype | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.media | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.media.extension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | DiagnosticReport.media.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | DiagnosticReport.media.modifierExtension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | DiagnosticReport.media.modifierExtension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | DiagnosticReport.media.comment | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.media.link | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.conclusion | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.conclusionCode | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | DiagnosticReport.presentedForm | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) |
IG © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
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