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Logical Model: Genomic Study

Official URL: http://hl7.org/fhir/uv/cg-model/StructureDefinition/GenomicStudy Version: 0.1.0
Draft as of 2022-03-10 Computable Name: GenomicStudy

A Genomic Study is a set of files and procedures that are performed to generate and analyze genomic data.

Formal Views of Profile Content

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

This structure is derived from DomainResource

Summary

Mandatory: 0 element (1 nested mandatory element)

This structure is derived from DomainResource

NameFlagsCard.TypeDescription & Constraintsdoco
.. GenomicStudy 0..*DomainResourceGenomic Study
... identifier 0..1IdentifierAn identifier for this genomic study
... status 0..1CodeableConceptThe status of the genomic study
... type 0..1CodeableConceptThe type of the study
... encounter 0..1Reference(Encounter)The healthcare encounter with which this genomics study is associated
... startDate 0..1dateTimeWhen the genomic study was started
... basedOn 0..*Reference(ServiceRequest | Task)Event resources that the genomic study is based on
... referrer 0..1Reference(Practitioner | PractitionerRole)Healthcare professional(s) who requested or referred the genomic study
... interpreter 0..*Reference(Practitioner | PractitionerRole)Healthcare professional(s) who interpreted the genomic study
... endpoint 0..*EndpointThe endpoint for the genomic study
... reason[x] 0..*Why the genomic study was performed
.... reasonCodeableConceptCodeableConcept
.... reasonReferenceReference(Condition | Observation)
... note 0..*AnnotationUser-defined notes related to the genomic study
... description 0..1stringA description of the genomic study
... genomicAnalysis 0..*BackboneElementGenomic Analysis
.... identifier 0..*IdentifierIdentifier(s) for the analysis
.... methodType 0..*CodeableConceptType of the method(s) used in the analysis
.... protocolDefinition 0..*Reference(ActivityDefinition)The defined protocol that describes the analysis
.... protocolPerformed 0..*Reference(Procedure)The protocol that was actually performed for the analysis
.... performer 0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | Device | RelatedPerson)The organization, healthcare professional(s), or others who participated in performing this study
.... device 0..*DeviceThe device(s) used for the analysis (e.g., sequencers)
.... genomicFile 0..*Reference(DocumentReference)Genomic data file(s) used in the analysis
.... genomicAssay 0..*BackboneElementGenomic Assay
..... identifier 0..*IdentifierIdentifier(s) for the assay
..... specimen 0..1Reference(Specimen)The specimen used in the assay
..... subject 0..1Reference(Patient)The subject of the assay
..... date 0..1dateTimeThe date of the assay
..... regionStudied 0..1Reference(DocumentReference)Genomic region studied by the assay
..... genomicFile 0..*Reference(DocumentReference)File(s) containing genomic data generated by the assay

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. GenomicStudy 0..*DomainResourceGenomic Study
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages: A human language.

... contained 0..*ResourceContained, inline Resources
... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... Slices for modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
Slice: Unordered, Open by value:url
... identifier 0..1IdentifierAn identifier for this genomic study
... status 0..1CodeableConceptThe status of the genomic study
... type 0..1CodeableConceptThe type of the study
... subject 1..1Reference(Patient)The subject of the genomic study
... encounter 0..1Reference(Encounter)The healthcare encounter with which this genomics study is associated
... startDate 0..1dateTimeWhen the genomic study was started
... basedOn 0..*Reference(ServiceRequest | Task)Event resources that the genomic study is based on
... referrer 0..1Reference(Practitioner | PractitionerRole)Healthcare professional(s) who requested or referred the genomic study
... interpreter 0..*Reference(Practitioner | PractitionerRole)Healthcare professional(s) who interpreted the genomic study
... endpoint 0..*EndpointThe endpoint for the genomic study
... reason[x] 0..*Why the genomic study was performed
.... reasonCodeableConceptCodeableConcept
.... reasonReferenceReference(Condition | Observation)
... note 0..*AnnotationUser-defined notes related to the genomic study
... description 0..1stringA description of the genomic study
... genomicAnalysis 0..*BackboneElementGenomic Analysis
.... identifier 0..*IdentifierIdentifier(s) for the analysis
.... methodType 0..*CodeableConceptType of the method(s) used in the analysis
.... protocolDefinition 0..*Reference(ActivityDefinition)The defined protocol that describes the analysis
.... protocolPerformed 0..*Reference(Procedure)The protocol that was actually performed for the analysis
.... performer 0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | Device | RelatedPerson)The organization, healthcare professional(s), or others who participated in performing this study
.... device 0..*DeviceThe device(s) used for the analysis (e.g., sequencers)
.... genomicFile 0..*Reference(DocumentReference)Genomic data file(s) used in the analysis
.... genomicAssay 0..*BackboneElementGenomic Assay
..... identifier 0..*IdentifierIdentifier(s) for the assay
..... specimen 0..1Reference(Specimen)The specimen used in the assay
..... subject 0..1Reference(Patient)The subject of the assay
..... date 0..1dateTimeThe date of the assay
..... regionStudied 0..1Reference(DocumentReference)Genomic region studied by the assay
..... genomicFile 0..*Reference(DocumentReference)File(s) containing genomic data generated by the assay

doco Documentation for this format

This structure is derived from DomainResource

Summary

Mandatory: 0 element (1 nested mandatory element)

Differential View

This structure is derived from DomainResource

NameFlagsCard.TypeDescription & Constraintsdoco
.. GenomicStudy 0..*DomainResourceGenomic Study
... identifier 0..1IdentifierAn identifier for this genomic study
... status 0..1CodeableConceptThe status of the genomic study
... type 0..1CodeableConceptThe type of the study
... encounter 0..1Reference(Encounter)The healthcare encounter with which this genomics study is associated
... startDate 0..1dateTimeWhen the genomic study was started
... basedOn 0..*Reference(ServiceRequest | Task)Event resources that the genomic study is based on
... referrer 0..1Reference(Practitioner | PractitionerRole)Healthcare professional(s) who requested or referred the genomic study
... interpreter 0..*Reference(Practitioner | PractitionerRole)Healthcare professional(s) who interpreted the genomic study
... endpoint 0..*EndpointThe endpoint for the genomic study
... reason[x] 0..*Why the genomic study was performed
.... reasonCodeableConceptCodeableConcept
.... reasonReferenceReference(Condition | Observation)
... note 0..*AnnotationUser-defined notes related to the genomic study
... description 0..1stringA description of the genomic study
... genomicAnalysis 0..*BackboneElementGenomic Analysis
.... identifier 0..*IdentifierIdentifier(s) for the analysis
.... methodType 0..*CodeableConceptType of the method(s) used in the analysis
.... protocolDefinition 0..*Reference(ActivityDefinition)The defined protocol that describes the analysis
.... protocolPerformed 0..*Reference(Procedure)The protocol that was actually performed for the analysis
.... performer 0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | Device | RelatedPerson)The organization, healthcare professional(s), or others who participated in performing this study
.... device 0..*DeviceThe device(s) used for the analysis (e.g., sequencers)
.... genomicFile 0..*Reference(DocumentReference)Genomic data file(s) used in the analysis
.... genomicAssay 0..*BackboneElementGenomic Assay
..... identifier 0..*IdentifierIdentifier(s) for the assay
..... specimen 0..1Reference(Specimen)The specimen used in the assay
..... subject 0..1Reference(Patient)The subject of the assay
..... date 0..1dateTimeThe date of the assay
..... regionStudied 0..1Reference(DocumentReference)Genomic region studied by the assay
..... genomicFile 0..*Reference(DocumentReference)File(s) containing genomic data generated by the assay

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. GenomicStudy 0..*DomainResourceGenomic Study
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages: A human language.

... contained 0..*ResourceContained, inline Resources
... Slices for extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
... Slices for modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
Slice: Unordered, Open by value:url
... identifier 0..1IdentifierAn identifier for this genomic study
... status 0..1CodeableConceptThe status of the genomic study
... type 0..1CodeableConceptThe type of the study
... subject 1..1Reference(Patient)The subject of the genomic study
... encounter 0..1Reference(Encounter)The healthcare encounter with which this genomics study is associated
... startDate 0..1dateTimeWhen the genomic study was started
... basedOn 0..*Reference(ServiceRequest | Task)Event resources that the genomic study is based on
... referrer 0..1Reference(Practitioner | PractitionerRole)Healthcare professional(s) who requested or referred the genomic study
... interpreter 0..*Reference(Practitioner | PractitionerRole)Healthcare professional(s) who interpreted the genomic study
... endpoint 0..*EndpointThe endpoint for the genomic study
... reason[x] 0..*Why the genomic study was performed
.... reasonCodeableConceptCodeableConcept
.... reasonReferenceReference(Condition | Observation)
... note 0..*AnnotationUser-defined notes related to the genomic study
... description 0..1stringA description of the genomic study
... genomicAnalysis 0..*BackboneElementGenomic Analysis
.... identifier 0..*IdentifierIdentifier(s) for the analysis
.... methodType 0..*CodeableConceptType of the method(s) used in the analysis
.... protocolDefinition 0..*Reference(ActivityDefinition)The defined protocol that describes the analysis
.... protocolPerformed 0..*Reference(Procedure)The protocol that was actually performed for the analysis
.... performer 0..*Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | Device | RelatedPerson)The organization, healthcare professional(s), or others who participated in performing this study
.... device 0..*DeviceThe device(s) used for the analysis (e.g., sequencers)
.... genomicFile 0..*Reference(DocumentReference)Genomic data file(s) used in the analysis
.... genomicAssay 0..*BackboneElementGenomic Assay
..... identifier 0..*IdentifierIdentifier(s) for the assay
..... specimen 0..1Reference(Specimen)The specimen used in the assay
..... subject 0..1Reference(Patient)The subject of the assay
..... date 0..1dateTimeThe date of the assay
..... regionStudied 0..1Reference(DocumentReference)Genomic region studied by the assay
..... genomicFile 0..*Reference(DocumentReference)File(s) containing genomic data generated by the assay

doco Documentation for this format

 

Other representations of profile: CSV, Excel

Terminology Bindings

PathConformanceValueSet
GenomicStudy.languagepreferredCommonLanguages
Max Binding: AllLanguages

Constraints

IdGradePathDetailsRequirements
dom-2errorGenomicStudyIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-3errorGenomicStudyIf 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-4errorGenomicStudyIf 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-5errorGenomicStudyIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6Best PracticeGenomicStudyA resource should have narrative for robust management
: text.`div`.exists()
ele-1errorGenomicStudy.metaAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorGenomicStudy.implicitRulesAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorGenomicStudy.languageAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorGenomicStudy.textAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1errorGenomicStudy.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorGenomicStudy.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1errorGenomicStudy.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1errorGenomicStudy.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()