Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide
3.0.0 - release
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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
| Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis | Version: 3.0.0 | |||
| Active as of 2024-11-19 | Computable Name: GenomicStudyAnalysis | |||
A genomic study analysis is a component of a genomic study.
This profile is only to be used as referenced by a genomic study instance. A Genomic Study Analysis makes no sense outside the context of a Genomic Study). Please refer to the Genomic Study profile for a description of genomic study and genomic study analysis.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from Procedure
| Path | Conformance | ValueSet / Code | URI |
| Procedure.status | required | Pattern: completedhttp://hl7.org/fhir/ValueSet/event-status|4.0.1from the FHIR Standard | |
| Procedure.category | example | ProcedureCategoryCodes(SNOMEDCT)http://hl7.org/fhir/ValueSet/procedure-categoryfrom the FHIR Standard |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Procedure | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Procedure | 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 | Procedure | 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 | Procedure | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Procedure | 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 | ||||
|---|---|---|---|---|---|---|---|---|
  Procedure |
0..* | Procedure | An action that is being or was performed on a patient | |||||
  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 | |||||
  Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
   method-type |
0..* | CodeableConcept | GenomicStudy.analysis.methodType URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type Binding: Genomic Study Method Type ValueSet (preferred) | |||||
| change-type |
0..* | CodeableConcept | GenomicStudy.analysis.changeType URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type Binding: Genomic Study Change Type ValueSet (preferred) | |||||
| genome-build |
0..1 | CodeableConcept | GenomicStudy.analysis.genomeBuild URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build Binding: LOINC Answer List LL1040-6 (extensible) | |||||
| genomic-source-class |
0..1 | CodeableConcept | GenomicStudy.analysis.genomicSourceClass URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genomic-source-class Binding: LOINC Answer List LL378-1 (extensible) | |||||
| title |
0..1 | string | GenomicStudy.analysis.title URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-title | |||||
| focus |
0..* | Reference(Resource) | GenomicStudy.analysis.focus URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus | |||||
| specimen |
0..* | Reference(Specimen) | GenomicStudy.analysis.specimen URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen | |||||
| metrics |
0..1 | (Complex) | Genomic Study Analysis Metrics URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics | |||||
| regions |
0..1 | (Complex) | Genomic Study Analysis Regions URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions | |||||
| device |
0..* | (Complex) | GenomicStudy.analysis.device URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device | |||||
| protocol-performed |
0..1 | Reference(Procedure | Task) | GenomicStudy.protocolPerformed URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-protocol-performed | |||||
| input |
0..* | (Complex) | GenomicStudy.analysis.input URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input | |||||
 output |
0..* | (Complex) | GenomicStudy.analysis.output URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output | |||||
 modifierExtension |
?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
Σ | 0..* | Identifier | GenomicStudy.analysis.identifier | ||||
| instantiatesCanonical |
Σ | 0..* | canonical(PlanDefinition | ActivityDefinition) | GenomicStudy.analysis.instantiatesCanonical | ||||
| instantiatesUri |
Σ | 0..* | uri | GenomicStudy.analysis.instantiatesUri | ||||
| status |
?!Σ | 1..1 | code | preparation | in-progress | not-done | on-hold | stopped | completed | entered-in-error | unknown Binding: EventStatus (required): A code specifying the state of the procedure. Required Pattern: completed | ||||
| category |
Σ | 1..1 | CodeableConcept | Classification of the procedure Binding: ProcedureCategoryCodes(SNOMEDCT) (example): A code that classifies a procedure for searching, sorting and display purposes. | ||||
| 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..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/observation-category | |||||
| version |
0..1 | string | Version of the system - if relevant | |||||
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| 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 | ||||
 subject |
Σ | 1..1 | Reference(Patient | Group) | Who the procedure was performed on | ||||
| performed[x] |
Σ | 0..1 | dateTime | GenomicStudy.analysis.date | ||||
| performer |
Σ | 0..* | BackboneElement | The people who performed the procedure | ||||
| 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 | ||||
| function |
Σ | 0..1 | CodeableConcept | GenomicStudy.analysis.performer.role Binding: ProcedurePerformerRoleCodes (example): A code that identifies the role of a performer of the procedure. | ||||
| actor |
Σ | 1..1 | Reference(Practitioner | PractitionerRole | Organization | Device) | GenomicStudy.analysis.performer.actor | ||||
| onBehalfOf |
0..1 | Reference(Organization) | Organization the device or practitioner was acting for | |||||
| note |
0..* | Annotation | GenomicStudy.analysis.note | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | URI | |||
| Procedure.language | preferred | CommonLanguages
http://hl7.org/fhir/ValueSet/languagesfrom the FHIR Standard | ||||
| Procedure.status | required | Pattern: completedhttp://hl7.org/fhir/ValueSet/event-status|4.0.1from the FHIR Standard | ||||
| Procedure.category | example | ProcedureCategoryCodes(SNOMEDCT)http://hl7.org/fhir/ValueSet/procedure-categoryfrom the FHIR Standard | ||||
| Procedure.performer.function | example | ProcedurePerformerRoleCodeshttp://hl7.org/fhir/ValueSet/performer-rolefrom the FHIR Standard | ||||
| Procedure.focalDevice.action | preferred | ProcedureDeviceActionCodeshttp://hl7.org/fhir/ValueSet/device-actionfrom the FHIR Standard |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Procedure | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Procedure | 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 | Procedure | 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 | Procedure | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Procedure | 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 Procedure
Summary
Mandatory: 2 elements
Prohibited: 19 elements
Extensions
This structure refers to these extensions:
Differential View
This structure is derived from Procedure
Key Elements View
| Path | Conformance | ValueSet / Code | URI |
| Procedure.status | required | Pattern: completedhttp://hl7.org/fhir/ValueSet/event-status|4.0.1from the FHIR Standard | |
| Procedure.category | example | ProcedureCategoryCodes(SNOMEDCT)http://hl7.org/fhir/ValueSet/procedure-categoryfrom the FHIR Standard |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Procedure | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Procedure | 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 | Procedure | 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 | Procedure | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Procedure | 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 | ||||
|---|---|---|---|---|---|---|---|---|
| Procedure |
0..* | Procedure | An action that is being or was performed on a patient | |||||
| 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 | |||||
| Slices for extension |
0..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| method-type |
0..* | CodeableConcept | GenomicStudy.analysis.methodType URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-method-type Binding: Genomic Study Method Type ValueSet (preferred) | |||||
| change-type |
0..* | CodeableConcept | GenomicStudy.analysis.changeType URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-change-type Binding: Genomic Study Change Type ValueSet (preferred) | |||||
| genome-build |
0..1 | CodeableConcept | GenomicStudy.analysis.genomeBuild URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genome-build Binding: LOINC Answer List LL1040-6 (extensible) | |||||
| genomic-source-class |
0..1 | CodeableConcept | GenomicStudy.analysis.genomicSourceClass URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-genomic-source-class Binding: LOINC Answer List LL378-1 (extensible) | |||||
| title |
0..1 | string | GenomicStudy.analysis.title URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-title | |||||
| focus |
0..* | Reference(Resource) | GenomicStudy.analysis.focus URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-focus | |||||
| specimen |
0..* | Reference(Specimen) | GenomicStudy.analysis.specimen URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-specimen | |||||
| metrics |
0..1 | (Complex) | Genomic Study Analysis Metrics URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-metrics | |||||
| regions |
0..1 | (Complex) | Genomic Study Analysis Regions URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-regions | |||||
| device |
0..* | (Complex) | GenomicStudy.analysis.device URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-device | |||||
| protocol-performed |
0..1 | Reference(Procedure | Task) | GenomicStudy.protocolPerformed URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-protocol-performed | |||||
| input |
0..* | (Complex) | GenomicStudy.analysis.input URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-input | |||||
| output |
0..* | (Complex) | GenomicStudy.analysis.output URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis-output | |||||
| modifierExtension |
?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
Σ | 0..* | Identifier | GenomicStudy.analysis.identifier | ||||
| instantiatesCanonical |
Σ | 0..* | canonical(PlanDefinition | ActivityDefinition) | GenomicStudy.analysis.instantiatesCanonical | ||||
| instantiatesUri |
Σ | 0..* | uri | GenomicStudy.analysis.instantiatesUri | ||||
| status |
?!Σ | 1..1 | code | preparation | in-progress | not-done | on-hold | stopped | completed | entered-in-error | unknown Binding: EventStatus (required): A code specifying the state of the procedure. Required Pattern: completed | ||||
| category |
Σ | 1..1 | CodeableConcept | Classification of the procedure Binding: ProcedureCategoryCodes(SNOMEDCT) (example): A code that classifies a procedure for searching, sorting and display purposes. | ||||
| 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..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/observation-category | |||||
| version |
0..1 | string | Version of the system - if relevant | |||||
| code |
1..1 | code | Symbol in syntax defined by the system Fixed Value: laboratory | |||||
| 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 | ||||
| subject |
Σ | 1..1 | Reference(Patient | Group) | Who the procedure was performed on | ||||
| performed[x] |
Σ | 0..1 | dateTime | GenomicStudy.analysis.date | ||||
| performer |
Σ | 0..* | BackboneElement | The people who performed the procedure | ||||
| 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 | ||||
| function |
Σ | 0..1 | CodeableConcept | GenomicStudy.analysis.performer.role Binding: ProcedurePerformerRoleCodes (example): A code that identifies the role of a performer of the procedure. | ||||
| actor |
Σ | 1..1 | Reference(Practitioner | PractitionerRole | Organization | Device) | GenomicStudy.analysis.performer.actor | ||||
| onBehalfOf |
0..1 | Reference(Organization) | Organization the device or practitioner was acting for | |||||
| note |
0..* | Annotation | GenomicStudy.analysis.note | |||||
| Documentation for this format | ||||||||
| Path | Conformance | ValueSet / Code | URI | |||
| Procedure.language | preferred | CommonLanguages
http://hl7.org/fhir/ValueSet/languagesfrom the FHIR Standard | ||||
| Procedure.status | required | Pattern: completedhttp://hl7.org/fhir/ValueSet/event-status|4.0.1from the FHIR Standard | ||||
| Procedure.category | example | ProcedureCategoryCodes(SNOMEDCT)http://hl7.org/fhir/ValueSet/procedure-categoryfrom the FHIR Standard | ||||
| Procedure.performer.function | example | ProcedurePerformerRoleCodeshttp://hl7.org/fhir/ValueSet/performer-rolefrom the FHIR Standard | ||||
| Procedure.focalDevice.action | preferred | ProcedureDeviceActionCodeshttp://hl7.org/fhir/ValueSet/device-actionfrom the FHIR Standard |
| Id | Grade | Path(s) | Details | Requirements |
| dom-2 | error | Procedure | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-3 | error | Procedure | 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 | Procedure | 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 | Procedure | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | best practice | Procedure | 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 Procedure
Summary
Mandatory: 2 elements
Prohibited: 19 elements
Extensions
This structure refers to these extensions:
Other representations of profile: CSV, Excel, Schematron
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-11-19
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