Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

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

Resource Profile: Genomic Study Analysis

Official URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study-analysis Version: 3.0.1-SNAPSHOT
Active as of 2024-05-15 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:

Formal Views of Profile Content

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

This structure is derived from Procedure

NameFlagsCard.TypeDescription & Constraintsdoco
.. Procedure 0..* Procedure An action that is being or was performed on a patient
... 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
... identifier 0..* Identifier GenomicStudy.analysis.identifier
... instantiatesCanonical 0..* canonical(PlanDefinition | ActivityDefinition) GenomicStudy.analysis.instantiatesCanonical
... instantiatesUri 0..* uri GenomicStudy.analysis.instantiatesUri
... basedOn 0..0
... partOf 0..0
... status 1..1 code preparation | in-progress | not-done | on-hold | stopped | completed | entered-in-error | unknown
Required Pattern: completed
... statusReason 0..0
... category 1..1 CodeableConcept Classification of the procedure
.... coding 1..1 Coding Code defined by a terminology system
Required Pattern: At least the following
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
... code 0..0
... encounter 0..0
... performed[x] 0..1 dateTime GenomicStudy.analysis.date
... recorder 0..0
... asserter 0..0
... performer
.... function 0..1 CodeableConcept GenomicStudy.analysis.performer.role
.... actor 1..1 Reference(Practitioner | PractitionerRole | Organization | Device) GenomicStudy.analysis.performer.actor
... location 0..0
... reasonCode 0..0
... reasonReference 0..0
... bodySite 0..0
... outcome 0..0
... report 0..0
... complication 0..0
... complicationDetail 0..0
... followUp 0..0
... note 0..* Annotation GenomicStudy.analysis.note
... focalDevice 0..0
... usedReference 0..0
... usedCode 0..0

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Procedure 0..* Procedure An action that is being or was performed on a patient
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... 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
... 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.

.... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
... subject Σ 1..1 Reference(Patient | Group) Who the procedure was performed on
... performed[x] Σ 0..1 dateTime GenomicStudy.analysis.date
... note 0..* Annotation GenomicStudy.analysis.note

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Procedure.statusrequiredPattern: completed
http://hl7.org/fhir/ValueSet/event-status|4.0.1
from the FHIR Standard
Procedure.categoryexampleProcedureCategoryCodes(SNOMEDCT)
http://hl7.org/fhir/ValueSet/procedure-category
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorProcedureIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorProcedureIf 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-4errorProcedureIf 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-5errorProcedureIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceProcedureA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()
NameFlagsCard.TypeDescription & Constraintsdoco
.. 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
... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Procedure.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
Procedure.statusrequiredPattern: completed
http://hl7.org/fhir/ValueSet/event-status|4.0.1
from the FHIR Standard
Procedure.categoryexampleProcedureCategoryCodes(SNOMEDCT)
http://hl7.org/fhir/ValueSet/procedure-category
from the FHIR Standard
Procedure.performer.functionexampleProcedurePerformerRoleCodes
http://hl7.org/fhir/ValueSet/performer-role
from the FHIR Standard
Procedure.focalDevice.actionpreferredProcedureDeviceActionCodes
http://hl7.org/fhir/ValueSet/device-action
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorProcedureIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorProcedureIf 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-4errorProcedureIf 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-5errorProcedureIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceProcedureA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

Differential View

This structure is derived from Procedure

NameFlagsCard.TypeDescription & Constraintsdoco
.. Procedure 0..* Procedure An action that is being or was performed on a patient
... 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
... identifier 0..* Identifier GenomicStudy.analysis.identifier
... instantiatesCanonical 0..* canonical(PlanDefinition | ActivityDefinition) GenomicStudy.analysis.instantiatesCanonical
... instantiatesUri 0..* uri GenomicStudy.analysis.instantiatesUri
... basedOn 0..0
... partOf 0..0
... status 1..1 code preparation | in-progress | not-done | on-hold | stopped | completed | entered-in-error | unknown
Required Pattern: completed
... statusReason 0..0
... category 1..1 CodeableConcept Classification of the procedure
.... coding 1..1 Coding Code defined by a terminology system
Required Pattern: At least the following
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
... code 0..0
... encounter 0..0
... performed[x] 0..1 dateTime GenomicStudy.analysis.date
... recorder 0..0
... asserter 0..0
... performer
.... function 0..1 CodeableConcept GenomicStudy.analysis.performer.role
.... actor 1..1 Reference(Practitioner | PractitionerRole | Organization | Device) GenomicStudy.analysis.performer.actor
... location 0..0
... reasonCode 0..0
... reasonReference 0..0
... bodySite 0..0
... outcome 0..0
... report 0..0
... complication 0..0
... complicationDetail 0..0
... followUp 0..0
... note 0..* Annotation GenomicStudy.analysis.note
... focalDevice 0..0
... usedReference 0..0
... usedCode 0..0

doco Documentation for this format

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Procedure 0..* Procedure An action that is being or was performed on a patient
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... 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
... 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.

.... coding Σ 1..1 Coding Code defined by a terminology system

Required Pattern: At least the following
..... system 1..1 uri Identity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... code 1..1 code Symbol in syntax defined by the system
Fixed Value: laboratory
... subject Σ 1..1 Reference(Patient | Group) Who the procedure was performed on
... performed[x] Σ 0..1 dateTime GenomicStudy.analysis.date
... note 0..* Annotation GenomicStudy.analysis.note

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Procedure.statusrequiredPattern: completed
http://hl7.org/fhir/ValueSet/event-status|4.0.1
from the FHIR Standard
Procedure.categoryexampleProcedureCategoryCodes(SNOMEDCT)
http://hl7.org/fhir/ValueSet/procedure-category
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorProcedureIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorProcedureIf 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-4errorProcedureIf 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-5errorProcedureIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceProcedureA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. 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
... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet / CodeURI
Procedure.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
Procedure.statusrequiredPattern: completed
http://hl7.org/fhir/ValueSet/event-status|4.0.1
from the FHIR Standard
Procedure.categoryexampleProcedureCategoryCodes(SNOMEDCT)
http://hl7.org/fhir/ValueSet/procedure-category
from the FHIR Standard
Procedure.performer.functionexampleProcedurePerformerRoleCodes
http://hl7.org/fhir/ValueSet/performer-role
from the FHIR Standard
Procedure.focalDevice.actionpreferredProcedureDeviceActionCodes
http://hl7.org/fhir/ValueSet/device-action
from the FHIR Standard

Constraints

IdGradePath(s)DetailsRequirements
dom-2errorProcedureIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorProcedureIf 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-4errorProcedureIf 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-5errorProcedureIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6best practiceProcedureA resource should have narrative for robust management
: text.`div`.exists()
ele-1error**ALL** elementsAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1error**ALL** extensionsMust have either extensions or value[x], not both
: extension.exists() != value.exists()

 

Other representations of profile: CSV, Excel, Schematron