HLA Reporting Implementation Guide
0.0.1 - Draft

This page is part of the HLA Reporting Implementation Guide (v0.0.1: Trial Use: 1) based on FHIR R4. This is the current published version. For a full list of available versions, see the Directory of published versions

StructureDefinition: HLAallele

HLA Allele profile of haplotype observation

The official URL for this profile is:

http://fhir.nmdp.org/ig/hla-reporting/StructureDefinition/hla-allele

Formal Views of Profile Content

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

This structure is derived from Haplotype

Summary

Mandatory: 3 elements
Must-Support: 1 element
Prohibited: 5 elements

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element Observation.derivedFrom is sliced based on the value of pattern:resolve().code

This structure is derived from Haplotype

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*HaplotypeHaplotype
... value[x] 1..1CodeableConceptActual result
... valueCodeableConcept 1..1CodeableConceptHaplotype name/code
Required Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://glstring.org
... referenceRange 0..0
.... derivedFrom:haplotype 0..0
.... derivedFrom:variant 0..0
.... derivedFrom:hla-sequence 0..*Reference(HLA Molecular Sequence)Related measurements the observation is made from
... component 1..*BackboneElementComponent results
... component:gene-studied S1..1BackboneElementGene studied ID
.... value[x] 1..1CodeableConceptIf no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HLA Gene Name Value Set (required)
... component:cytogenetic-location 0..0
... component:ref-sequence-assembly 0..0

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*HaplotypeHaplotype
... id Σ0..1stringLogical id of this artifact
... meta ΣI0..1MetaMetadata about the resource
... implicitRules ?!ΣI0..1uriA set of rules under which this content was created
... language I0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension I0..*ExtensionExtension
Slice: Unordered, Open by value:url
... bodySite I0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... observation-secondaryFinding I0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible)
... modifierExtension ?!I0..*ExtensionExtensions that cannot be ignored
... identifier ΣI0..*IdentifierBusiness Identifier for observation
... basedOn ΣI0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf ΣI0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!ΣI1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category I1..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred)

Required Pattern: At least the following
.... id0..1stringUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... code ΣI1..1CodeableConceptType of observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: At least the following
.... id0..1stringUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 84414-2
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject ΣI0..1Reference(Patient | Group | Location)Who and/or what the observation is about
... focus ΣI0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter ΣI0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] ΣI0..1(Slice Definition)Clinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime ΣI0..1dateTimeClinically relevant time/time-period for observation
... issued ΣI0..1instantDate/Time this version was made available
... performer ΣI0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ΣI1..1(Slice Definition)Actual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣI1..1CodeableConceptHaplotype name/code
Binding: (unbound) (example)
Required Pattern: At least the following
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://glstring.org
...... version0..1stringVersion of the system - if relevant
...... code0..1codeSymbol in syntax defined by the system
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text0..1stringPlain text representation of the concept
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... note I0..*AnnotationComments about the observation
... bodySite I0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example)
... method I0..1CodeableConceptHaplotype determination method
Binding: LOINC Answer List LL4050-2 (extensible)
... specimen I0..1Reference(Specimen)Specimen examined
... device I0..1Reference(Device | DeviceMetric)(Measurement) Device
... hasMember ΣI0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom ΣI0..*(Slice Definition)Related measurements the observation is made from
Slice: Unordered, Open by pattern:resolve().code
.... derivedFrom:hla-sequence ΣI0..*Reference(HLA Molecular Sequence)Related measurements the observation is made from
... component ΣI1..*(Slice Definition)Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... value[x] ΣI0..1Actual component result
...... valueQuantityQuantity
...... valueCodeableConceptCodeableConcept
...... valueStringstring
...... valueBooleanboolean
...... valueIntegerinteger
...... valueRangeRange
...... valueRatioRatio
...... valueSampledDataSampledData
...... valueTimetime
...... valueDateTimedateTime
...... valuePeriodPeriod
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:gene-studied SΣI1..1BackboneElementGene studied ID
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48018-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] ΣI1..1CodeableConceptIf no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HLA Gene Name Value Set (required)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result

doco Documentation for this format

This structure is derived from Haplotype

Summary

Mandatory: 3 elements
Must-Support: 1 element
Prohibited: 5 elements

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element Observation.derivedFrom is sliced based on the value of pattern:resolve().code

Differential View

This structure is derived from Haplotype

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*HaplotypeHaplotype
... value[x] 1..1CodeableConceptActual result
... valueCodeableConcept 1..1CodeableConceptHaplotype name/code
Required Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://glstring.org
... referenceRange 0..0
.... derivedFrom:haplotype 0..0
.... derivedFrom:variant 0..0
.... derivedFrom:hla-sequence 0..*Reference(HLA Molecular Sequence)Related measurements the observation is made from
... component 1..*BackboneElementComponent results
... component:gene-studied S1..1BackboneElementGene studied ID
.... value[x] 1..1CodeableConceptIf no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HLA Gene Name Value Set (required)
... component:cytogenetic-location 0..0
... component:ref-sequence-assembly 0..0

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*HaplotypeHaplotype
... id Σ0..1stringLogical id of this artifact
... meta ΣI0..1MetaMetadata about the resource
... implicitRules ?!ΣI0..1uriA set of rules under which this content was created
... language I0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension I0..*ExtensionExtension
Slice: Unordered, Open by value:url
... bodySite I0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... observation-secondaryFinding I0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible)
... modifierExtension ?!I0..*ExtensionExtensions that cannot be ignored
... identifier ΣI0..*IdentifierBusiness Identifier for observation
... basedOn ΣI0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf ΣI0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!ΣI1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category I1..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred)

Required Pattern: At least the following
.... id0..1stringUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... code ΣI1..1CodeableConceptType of observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: At least the following
.... id0..1stringUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 84414-2
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject ΣI0..1Reference(Patient | Group | Location)Who and/or what the observation is about
... focus ΣI0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter ΣI0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] ΣI0..1(Slice Definition)Clinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime ΣI0..1dateTimeClinically relevant time/time-period for observation
... issued ΣI0..1instantDate/Time this version was made available
... performer ΣI0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ΣI1..1(Slice Definition)Actual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣI1..1CodeableConceptHaplotype name/code
Binding: (unbound) (example)
Required Pattern: At least the following
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... system1..1uriIdentity of the terminology system
Fixed Value: http://glstring.org
...... version0..1stringVersion of the system - if relevant
...... code0..1codeSymbol in syntax defined by the system
...... display0..1stringRepresentation defined by the system
...... userSelected0..1booleanIf this coding was chosen directly by the user
..... text0..1stringPlain text representation of the concept
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... note I0..*AnnotationComments about the observation
... bodySite I0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example)
... method I0..1CodeableConceptHaplotype determination method
Binding: LOINC Answer List LL4050-2 (extensible)
... specimen I0..1Reference(Specimen)Specimen examined
... device I0..1Reference(Device | DeviceMetric)(Measurement) Device
... hasMember ΣI0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom ΣI0..*(Slice Definition)Related measurements the observation is made from
Slice: Unordered, Open by pattern:resolve().code
.... derivedFrom:hla-sequence ΣI0..*Reference(HLA Molecular Sequence)Related measurements the observation is made from
... component ΣI1..*(Slice Definition)Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... value[x] ΣI0..1Actual component result
...... valueQuantityQuantity
...... valueCodeableConceptCodeableConcept
...... valueStringstring
...... valueBooleanboolean
...... valueIntegerinteger
...... valueRangeRange
...... valueRatioRatio
...... valueSampledDataSampledData
...... valueTimetime
...... valueDateTimedateTime
...... valuePeriodPeriod
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:gene-studied SΣI1..1BackboneElementGene studied ID
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 48018-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] ΣI1..1CodeableConceptIf no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used.
Binding: HLA Gene Name Value Set (required)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result

doco Documentation for this format

 

Other representations of profile: Schematron

Terminology Bindings

Terminology Bindings

PathConformanceValueSet / Code
Observation.languagepreferredCommonLanguages
Max Binding: AllLanguages
Observation.statusrequiredObservationStatus
Observation.categorypreferredPattern: laboratory
Observation.codeexamplePattern: LOINC code 84414-2
Observation.value[x]:valueCodeableConceptexamplePattern: null
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.bodySiteexampleSNOMEDCTBodyStructures
Observation.methodextensibleLOINC LL4050-2
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component:gene-studied.codeexamplePattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]requiredHLAGeneIdVS
Observation.component:gene-studied.dataAbsentReasonextensibleDataAbsentReason
Observation.component:cytogenetic-location.codeexamplePattern: LOINC code 48001-2
Observation.component:cytogenetic-location.value[x]example
Observation.component:cytogenetic-location.dataAbsentReasonextensibleDataAbsentReason
Observation.component:ref-sequence-assembly.codeexamplePattern: LOINC code 62374-4
Observation.component:ref-sequence-assembly.value[x]extensibleLOINC LL1040-6
Observation.component:ref-sequence-assembly.dataAbsentReasonextensibleDataAbsentReason

Constraints

Constraints

IdPathDetailsRequirements