MatchSyncIG - Local Development build (v0.1.0). See the Directory of published versions

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Resource Profile: HLA_DRB1

Genotype for HLA-DRB1

Usage:

• Use this Resource Profile: MatchSync Bundle with Separate HLA
• Examples for this Resource Profile: Observation/HLA-DRB1-Example

Formal Views of Profile Content

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

• Differential Table
• Key Elements Table
• Snapshot Table
• Statistics/References
• All

This structure is derived from HLAGenotype

Name	Flags	Card.	Type	Description & Constraints
Observation		0..*	HLAGenotype	Genotype
component:gene-studied		1..*	BackboneElement	Gene Studied
valueCodeableConcept		1..1	CodeableConcept	The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://www.genenames.org/geneId
code		1..1	code	Symbol in syntax defined by the system Fixed Value: HGNC:4948
display		1..1	string	Representation defined by the system Fixed Value: HLA-DRB1
Documentation for this format

Name	Flags	Card.	Type	Description & Constraints
Observation	C	0..*	HLAGenotype	Genotype
meta	Σ	0..1	Meta	Metadata about the resource
Slices for security	Σ	1..*	Coding	Security Labels applied to this resource Slice: Unordered, Open by pattern:system Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System.
security:TransplantCenter	SΣ	1..1	Coding	Security Labels applied to this resource Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System.
system	Σ	1..1	uri	Identity of the terminology system Required Pattern: http://terminology.nmdp.org/codesystem/transplant-center
code	Σ	1..1	code	Symbol in syntax defined by the system
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
secondary-finding		0..1	CodeableConcept	Secondary 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): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding.
body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
status	?!Σ	1..1	code	registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category		1..*	CodeableConcept	Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
category:labCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
coding	Σ	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	Σ	1..1	CodeableConcept	84413-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 84413-4
subject	SΣ	1..1	Reference(MSPatient)	Who and/or what the observation is about
Slices for effective[x]	Σ	1..1	dateTime	Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this
effective[x]:effectiveDateTime	SΣ	1..1	dateTime	Clinically relevant time/time-period for observation
Slices for value[x]	ΣC	1..1	CodeableConcept	Genotype name Slice: Unordered, Closed by type:$this Binding: (unbound) (example): Binding not yet defined
value[x]:valueCodeableConcept	ΣC	1..1	CodeableConcept	Genotype name Binding: (unbound) (example): Binding not yet defined
Slices for coding	Σ	1..*	Coding	Code defined by a terminology system Slice: Unordered, Open by value:system
coding:GL	SΣ	1..1	Coding	Code defined by a terminology system
system	Σ	1..1	uri	Identity of the terminology system Fixed Value: http://glstring.org
code	ΣC	1..1	code	Symbol in syntax defined by the system
specimen	S	1..1	Reference(MSSpecimen)	Specimen used for this observation
Slices for derivedFrom	Σ	0..*	Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)	Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
derivedFrom:Haplotype	Σ	0..*	Reference(Haplotype)	Haplotype this genotype is derived from
derivedFrom:Variant	Σ	0..*	Reference(Variant)	Variant this genotype is derived from
Slices for component	Σ	1..*	BackboneElement	Component results Slice: Unordered, Open by pattern:code
component:All Slices				Content/Rules for all slices
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
component:conclusion-string	Σ	0..1	BackboneElement	Clinical Conclusion
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
code		1..1	code	Symbol in syntax defined by the system Fixed Value: conclusion-string
component:gene-studied	SΣ	1..*	BackboneElement	Gene Studied
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48018-6
value[x]	Σ	1..1	CodeableConcept	The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HLA Gene Name Value Set (required) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://www.genenames.org/geneId
code		1..1	code	Symbol in syntax defined by the system Fixed Value: HGNC:4948
display		1..1	string	Representation defined by the system Fixed Value: HLA-DRB1
component:cytogenetic-location	Σ	0..*	BackboneElement	Cytogenetic (Chromosome) Location
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48001-2
value[x]	Σ	1..1	CodeableConcept	Example: 1q21.1
component:reference-sequence-assembly	Σ	0..*	BackboneElement	Human Reference Sequence Assembly
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 62374-4
value[x]	Σ	1..1	CodeableConcept	GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet / Code
Observation.meta.security	extensible	All Security Labels
Observation.meta.security:TransplantCenter	extensible	All Security Labels
Observation.status	required	ObservationStatus
Observation.category	preferred	ObservationCategoryCodes
Observation.category:labCategory	preferred	ObservationCategoryCodes
Observation.code	example	Pattern: LOINC code 84413-4
Observation.value[x]	example
Observation.value[x]:valueCodeableConcept	example
Observation.component.code	example	LOINCCodes (a valid code from LOINC)
Observation.component:conclusion-string.code	example	Pattern: conclusion-string
Observation.component:gene-studied.code	example	Pattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]	required	​Pattern: HGNC:4948("HLA-DRB1")
Observation.component:cytogenetic-location.code	example	Pattern: LOINC code 48001-2
Observation.component:reference-sequence-assembly.code	example	Pattern: LOINC code 62374-4
Observation.component:reference-sequence-assembly.value[x]	extensible	LOINC LL1040-6

Constraints

Id	Grade	Path(s)	Details	Requirements
GLSC	warning	Observation.value[x]:valueCodeableConcept.coding:GL.code	Use GL String Code to report HLA genotype : matches('^hla#.+')
dom-2	error	Observation	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Observation	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	Observation	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	Observation	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Observation	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()
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

Name	Flags	Card.	Type	Description & Constraints
Observation	C	0..*	HLAGenotype	Genotype
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
versionId	Σ	0..1	id	Version specific identifier
lastUpdated	Σ	0..1	instant	When the resource version last changed
source	Σ	0..1	uri	Identifies where the resource comes from
profile	Σ	0..*	canonical(StructureDefinition)	Profiles this resource claims to conform to
Slices for security	Σ	1..*	Coding	Security Labels applied to this resource Slice: Unordered, Open by pattern:system Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System.
security:TransplantCenter	SΣ	1..1	Coding	Security Labels applied to this resource Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System.
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
system	Σ	1..1	uri	Identity of the terminology system Required Pattern: http://terminology.nmdp.org/codesystem/transplant-center
version	Σ	0..1	string	Version of the system - if relevant
code	Σ	1..1	code	Symbol in syntax defined by the system
display	Σ	0..1	string	Representation defined by the system
userSelected	Σ	0..1	boolean	If this coding was chosen directly by the user
tag	Σ	0..*	Coding	Tags applied to this resource Binding: CommonTags (example): Codes that represent various types of tags, commonly workflow-related; e.g. "Needs review by Dr. Jones".
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. Additional Bindings Purpose AllLanguages Max Binding
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
secondary-finding		0..1	CodeableConcept	Secondary 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): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding.
body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	Business Identifier for observation
basedOn	Σ	0..*	Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)	Fulfills plan, proposal or order
partOf	Σ	0..*	Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)	Part of referenced event
status	?!Σ	1..1	code	registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category		1..*	CodeableConcept	Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
category:labCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
coding	Σ	1..*	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/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
code	Σ	1..1	CodeableConcept	84413-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
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://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 84413-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
subject	SΣ	1..1	Reference(MSPatient)	Who and/or what the observation is about
focus	ΣTU	0..*	Reference(Resource)	What the observation is about, when it is not about the subject of record
encounter	Σ	0..1	Reference(Encounter)	Healthcare event during which this observation is made
Slices for effective[x]	Σ	1..1	dateTime	Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this
effective[x]:effectiveDateTime	SΣ	1..1	dateTime	Clinically relevant time/time-period for observation
issued	Σ	0..1	instant	Date/Time this version was made available
performer	Σ	0..*	Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)	Who is responsible for the observation
Slices for value[x]	ΣC	1..1	CodeableConcept	Genotype name Slice: Unordered, Closed by type:$this Binding: (unbound) (example): Binding not yet defined
value[x]:valueCodeableConcept	ΣC	1..1	CodeableConcept	Genotype name Binding: (unbound) (example): Binding not yet defined
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
Slices for coding	Σ	1..*	Coding	Code defined by a terminology system Slice: Unordered, Open by value:system
coding:GL	SΣ	1..1	Coding	Code defined by a terminology system
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
system	Σ	1..1	uri	Identity of the terminology system Fixed Value: http://glstring.org
version	Σ	0..1	string	Version of the system - if relevant
code	ΣC	1..1	code	Symbol in syntax defined by the system
display	Σ	0..1	string	Representation defined by the system
userSelected	Σ	0..1	boolean	If this coding was chosen directly by the user
text	Σ	0..1	string	Plain text representation of the concept
dataAbsentReason	C	0..1	CodeableConcept	Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
note		0..*	CodedAnnotation	Comments about the Observation that also contain a coded type
bodySite		0..1	CodeableConcept	Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
method		0..1	CodeableConcept	How it was done Binding: ObservationMethods (example): Methods for simple observations.
specimen	S	1..1	Reference(MSSpecimen)	Specimen used for this observation
device		0..1	Reference(Device | DeviceMetric)	(Measurement) Device
referenceRange	C	0..*	BackboneElement	Provides guide for interpretation
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
low	C	0..1	SimpleQuantity	Low Range, if relevant
high	C	0..1	SimpleQuantity	High Range, if relevant
type		0..1	CodeableConcept	Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
appliesTo		0..*	CodeableConcept	Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
age		0..1	Range	Applicable age range, if relevant
text		0..1	string	Text based reference range in an observation
hasMember	Σ	0..*	Reference(Observation | QuestionnaireResponse | MolecularSequence)	Related resource that belongs to the Observation group
Slices for derivedFrom	Σ	0..*	Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)	Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
derivedFrom:Haplotype	Σ	0..*	Reference(Haplotype)	Haplotype this genotype is derived from
derivedFrom:Variant	Σ	0..*	Reference(Variant)	Variant this genotype is derived from
Slices for component	Σ	1..*	BackboneElement	Component results Slice: Unordered, Open by pattern:code
component:All Slices				Content/Rules for all slices
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
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
value[x]	Σ	0..1		Actual component result
valueQuantity			Quantity
valueCodeableConcept			CodeableConcept
valueString			string
valueBoolean			boolean
valueInteger			integer
valueRange			Range
valueRatio			Ratio
valueSampledData			SampledData
valueTime			time
valueDateTime			dateTime
valuePeriod			Period
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:conclusion-string	Σ	0..1	BackboneElement	Clinical Conclusion
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
code	Σ	1..1	CodeableConcept	conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: conclusion-string
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	string	Summary conclusion (interpretation/impression)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:gene-studied	SΣ	1..*	BackboneElement	Gene Studied
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
code	Σ	1..1	CodeableConcept	48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
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://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48018-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HLA Gene Name Value Set (required) Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
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://www.genenames.org/geneId
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: HGNC:4948
display		1..1	string	Representation defined by the system Fixed Value: HLA-DRB1
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:cytogenetic-location	Σ	0..*	BackboneElement	Cytogenetic (Chromosome) Location
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
code	Σ	1..1	CodeableConcept	48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
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://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48001-2
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Example: 1q21.1
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:reference-sequence-assembly	Σ	0..*	BackboneElement	Human Reference Sequence Assembly
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
code	Σ	1..1	CodeableConcept	62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
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://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 62374-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet / Code
Observation.meta.security	extensible	All Security Labels
Observation.meta.security:TransplantCenter	extensible	All Security Labels
Observation.meta.tag	example	CommonTags
Observation.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding
Observation.status	required	ObservationStatus
Observation.category	preferred	ObservationCategoryCodes
Observation.category:labCategory	preferred	ObservationCategoryCodes
Observation.code	example	Pattern: LOINC code 84413-4
Observation.value[x]	example
Observation.value[x]:valueCodeableConcept	example
Observation.dataAbsentReason	extensible	DataAbsentReason
Observation.interpretation	extensible	ObservationInterpretationCodes
Observation.bodySite	example	SNOMEDCTBodyStructures
Observation.method	example	ObservationMethods
Observation.referenceRange.type	preferred	ObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesTo	example	ObservationReferenceRangeAppliesToCodes
Observation.component.code	example	LOINCCodes (a valid code from LOINC)
Observation.component.dataAbsentReason	extensible	DataAbsentReason
Observation.component.interpretation	extensible	ObservationInterpretationCodes
Observation.component:conclusion-string.code	example	Pattern: conclusion-string
Observation.component:conclusion-string.dataAbsentReason	extensible	DataAbsentReason
Observation.component:conclusion-string.interpretation	extensible	ObservationInterpretationCodes
Observation.component:gene-studied.code	example	Pattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]	required	​Pattern: HGNC:4948("HLA-DRB1")
Observation.component:gene-studied.dataAbsentReason	extensible	DataAbsentReason
Observation.component:gene-studied.interpretation	extensible	ObservationInterpretationCodes
Observation.component:cytogenetic-location.code	example	Pattern: LOINC code 48001-2
Observation.component:cytogenetic-location.dataAbsentReason	extensible	DataAbsentReason
Observation.component:cytogenetic-location.interpretation	extensible	ObservationInterpretationCodes
Observation.component:reference-sequence-assembly.code	example	Pattern: LOINC code 62374-4
Observation.component:reference-sequence-assembly.value[x]	extensible	LOINC LL1040-6
Observation.component:reference-sequence-assembly.dataAbsentReason	extensible	DataAbsentReason
Observation.component:reference-sequence-assembly.interpretation	extensible	ObservationInterpretationCodes

Constraints

Id	Grade	Path(s)	Details	Requirements
GLSC	warning	Observation.value[x]:valueCodeableConcept.coding:GL.code	Use GL String Code to report HLA genotype : matches('^hla#.+')
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()
obs-3	error	Observation.referenceRange	Must have at least a low or a high or text : low.exists() or high.exists() or text.exists()

This structure is derived from HLAGenotype

Summary

Mandatory: 1 element

Differential View

This structure is derived from HLAGenotype

Name	Flags	Card.	Type	Description & Constraints
Observation		0..*	HLAGenotype	Genotype
component:gene-studied		1..*	BackboneElement	Gene Studied
valueCodeableConcept		1..1	CodeableConcept	The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://www.genenames.org/geneId
code		1..1	code	Symbol in syntax defined by the system Fixed Value: HGNC:4948
display		1..1	string	Representation defined by the system Fixed Value: HLA-DRB1
Documentation for this format

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
Observation	C	0..*	HLAGenotype	Genotype
meta	Σ	0..1	Meta	Metadata about the resource
Slices for security	Σ	1..*	Coding	Security Labels applied to this resource Slice: Unordered, Open by pattern:system Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System.
security:TransplantCenter	SΣ	1..1	Coding	Security Labels applied to this resource Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System.
system	Σ	1..1	uri	Identity of the terminology system Required Pattern: http://terminology.nmdp.org/codesystem/transplant-center
code	Σ	1..1	code	Symbol in syntax defined by the system
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
secondary-finding		0..1	CodeableConcept	Secondary 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): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding.
body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
status	?!Σ	1..1	code	registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category		1..*	CodeableConcept	Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
category:labCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
coding	Σ	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	Σ	1..1	CodeableConcept	84413-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 84413-4
subject	SΣ	1..1	Reference(MSPatient)	Who and/or what the observation is about
Slices for effective[x]	Σ	1..1	dateTime	Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this
effective[x]:effectiveDateTime	SΣ	1..1	dateTime	Clinically relevant time/time-period for observation
Slices for value[x]	ΣC	1..1	CodeableConcept	Genotype name Slice: Unordered, Closed by type:$this Binding: (unbound) (example): Binding not yet defined
value[x]:valueCodeableConcept	ΣC	1..1	CodeableConcept	Genotype name Binding: (unbound) (example): Binding not yet defined
Slices for coding	Σ	1..*	Coding	Code defined by a terminology system Slice: Unordered, Open by value:system
coding:GL	SΣ	1..1	Coding	Code defined by a terminology system
system	Σ	1..1	uri	Identity of the terminology system Fixed Value: http://glstring.org
code	ΣC	1..1	code	Symbol in syntax defined by the system
specimen	S	1..1	Reference(MSSpecimen)	Specimen used for this observation
Slices for derivedFrom	Σ	0..*	Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)	Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
derivedFrom:Haplotype	Σ	0..*	Reference(Haplotype)	Haplotype this genotype is derived from
derivedFrom:Variant	Σ	0..*	Reference(Variant)	Variant this genotype is derived from
Slices for component	Σ	1..*	BackboneElement	Component results Slice: Unordered, Open by pattern:code
component:All Slices				Content/Rules for all slices
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
component:conclusion-string	Σ	0..1	BackboneElement	Clinical Conclusion
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
code		1..1	code	Symbol in syntax defined by the system Fixed Value: conclusion-string
component:gene-studied	SΣ	1..*	BackboneElement	Gene Studied
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48018-6
value[x]	Σ	1..1	CodeableConcept	The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HLA Gene Name Value Set (required) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://www.genenames.org/geneId
code		1..1	code	Symbol in syntax defined by the system Fixed Value: HGNC:4948
display		1..1	string	Representation defined by the system Fixed Value: HLA-DRB1
component:cytogenetic-location	Σ	0..*	BackboneElement	Cytogenetic (Chromosome) Location
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48001-2
value[x]	Σ	1..1	CodeableConcept	Example: 1q21.1
component:reference-sequence-assembly	Σ	0..*	BackboneElement	Human Reference Sequence Assembly
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 62374-4
value[x]	Σ	1..1	CodeableConcept	GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet / Code
Observation.meta.security	extensible	All Security Labels
Observation.meta.security:TransplantCenter	extensible	All Security Labels
Observation.status	required	ObservationStatus
Observation.category	preferred	ObservationCategoryCodes
Observation.category:labCategory	preferred	ObservationCategoryCodes
Observation.code	example	Pattern: LOINC code 84413-4
Observation.value[x]	example
Observation.value[x]:valueCodeableConcept	example
Observation.component.code	example	LOINCCodes (a valid code from LOINC)
Observation.component:conclusion-string.code	example	Pattern: conclusion-string
Observation.component:gene-studied.code	example	Pattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]	required	​Pattern: HGNC:4948("HLA-DRB1")
Observation.component:cytogenetic-location.code	example	Pattern: LOINC code 48001-2
Observation.component:reference-sequence-assembly.code	example	Pattern: LOINC code 62374-4
Observation.component:reference-sequence-assembly.value[x]	extensible	LOINC LL1040-6

Constraints

Id	Grade	Path(s)	Details	Requirements
GLSC	warning	Observation.value[x]:valueCodeableConcept.coding:GL.code	Use GL String Code to report HLA genotype : matches('^hla#.+')
dom-2	error	Observation	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Observation	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	Observation	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	Observation	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Observation	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()
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present : dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present : value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

Snapshot View

Name	Flags	Card.	Type	Description & Constraints
Observation	C	0..*	HLAGenotype	Genotype
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
versionId	Σ	0..1	id	Version specific identifier
lastUpdated	Σ	0..1	instant	When the resource version last changed
source	Σ	0..1	uri	Identifies where the resource comes from
profile	Σ	0..*	canonical(StructureDefinition)	Profiles this resource claims to conform to
Slices for security	Σ	1..*	Coding	Security Labels applied to this resource Slice: Unordered, Open by pattern:system Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System.
security:TransplantCenter	SΣ	1..1	Coding	Security Labels applied to this resource Binding: All Security Labels (extensible): Security Labels from the Healthcare Privacy and Security Classification System.
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
system	Σ	1..1	uri	Identity of the terminology system Required Pattern: http://terminology.nmdp.org/codesystem/transplant-center
version	Σ	0..1	string	Version of the system - if relevant
code	Σ	1..1	code	Symbol in syntax defined by the system
display	Σ	0..1	string	Representation defined by the system
userSelected	Σ	0..1	boolean	If this coding was chosen directly by the user
tag	Σ	0..*	Coding	Tags applied to this resource Binding: CommonTags (example): Codes that represent various types of tags, commonly workflow-related; e.g. "Needs review by Dr. Jones".
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. Additional Bindings Purpose AllLanguages Max Binding
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
secondary-finding		0..1	CodeableConcept	Secondary 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): Codes to denote a guideline or policy statement.when a genetic test result is being shared as a secondary finding.
body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	Business Identifier for observation
basedOn	Σ	0..*	Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)	Fulfills plan, proposal or order
partOf	Σ	0..*	Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)	Part of referenced event
status	?!Σ	1..1	code	registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category		1..*	CodeableConcept	Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
category:labCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
coding	Σ	1..*	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/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
code	Σ	1..1	CodeableConcept	84413-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
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://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 84413-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
subject	SΣ	1..1	Reference(MSPatient)	Who and/or what the observation is about
focus	ΣTU	0..*	Reference(Resource)	What the observation is about, when it is not about the subject of record
encounter	Σ	0..1	Reference(Encounter)	Healthcare event during which this observation is made
Slices for effective[x]	Σ	1..1	dateTime	Clinically relevant time/time-period for observation Slice: Unordered, Closed by type:$this
effective[x]:effectiveDateTime	SΣ	1..1	dateTime	Clinically relevant time/time-period for observation
issued	Σ	0..1	instant	Date/Time this version was made available
performer	Σ	0..*	Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)	Who is responsible for the observation
Slices for value[x]	ΣC	1..1	CodeableConcept	Genotype name Slice: Unordered, Closed by type:$this Binding: (unbound) (example): Binding not yet defined
value[x]:valueCodeableConcept	ΣC	1..1	CodeableConcept	Genotype name Binding: (unbound) (example): Binding not yet defined
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
Slices for coding	Σ	1..*	Coding	Code defined by a terminology system Slice: Unordered, Open by value:system
coding:GL	SΣ	1..1	Coding	Code defined by a terminology system
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
system	Σ	1..1	uri	Identity of the terminology system Fixed Value: http://glstring.org
version	Σ	0..1	string	Version of the system - if relevant
code	ΣC	1..1	code	Symbol in syntax defined by the system
display	Σ	0..1	string	Representation defined by the system
userSelected	Σ	0..1	boolean	If this coding was chosen directly by the user
text	Σ	0..1	string	Plain text representation of the concept
dataAbsentReason	C	0..1	CodeableConcept	Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
note		0..*	CodedAnnotation	Comments about the Observation that also contain a coded type
bodySite		0..1	CodeableConcept	Observed body part Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
method		0..1	CodeableConcept	How it was done Binding: ObservationMethods (example): Methods for simple observations.
specimen	S	1..1	Reference(MSSpecimen)	Specimen used for this observation
device		0..1	Reference(Device | DeviceMetric)	(Measurement) Device
referenceRange	C	0..*	BackboneElement	Provides guide for interpretation
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
low	C	0..1	SimpleQuantity	Low Range, if relevant
high	C	0..1	SimpleQuantity	High Range, if relevant
type		0..1	CodeableConcept	Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
appliesTo		0..*	CodeableConcept	Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
age		0..1	Range	Applicable age range, if relevant
text		0..1	string	Text based reference range in an observation
hasMember	Σ	0..*	Reference(Observation | QuestionnaireResponse | MolecularSequence)	Related resource that belongs to the Observation group
Slices for derivedFrom	Σ	0..*	Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)	Related measurements the observation is made from Slice: Unordered, Open by profile:resolve()
derivedFrom:Haplotype	Σ	0..*	Reference(Haplotype)	Haplotype this genotype is derived from
derivedFrom:Variant	Σ	0..*	Reference(Variant)	Variant this genotype is derived from
Slices for component	Σ	1..*	BackboneElement	Component results Slice: Unordered, Open by pattern:code
component:All Slices				Content/Rules for all slices
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
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
value[x]	Σ	0..1		Actual component result
valueQuantity			Quantity
valueCodeableConcept			CodeableConcept
valueString			string
valueBoolean			boolean
valueInteger			integer
valueRange			Range
valueRatio			Ratio
valueSampledData			SampledData
valueTime			time
valueDateTime			dateTime
valuePeriod			Period
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:conclusion-string	Σ	0..1	BackboneElement	Clinical Conclusion
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
code	Σ	1..1	CodeableConcept	conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: conclusion-string
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	string	Summary conclusion (interpretation/impression)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:gene-studied	SΣ	1..*	BackboneElement	Gene Studied
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
code	Σ	1..1	CodeableConcept	48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
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://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48018-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HLA Gene Name Value Set (required) Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
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://www.genenames.org/geneId
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: HGNC:4948
display		1..1	string	Representation defined by the system Fixed Value: HLA-DRB1
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:cytogenetic-location	Σ	0..*	BackboneElement	Cytogenetic (Chromosome) Location
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
code	Σ	1..1	CodeableConcept	48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
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://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48001-2
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Example: 1q21.1
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:reference-sequence-assembly	Σ	0..*	BackboneElement	Human Reference Sequence Assembly
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
code	Σ	1..1	CodeableConcept	62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (complex)
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://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 62374-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet / Code
Observation.meta.security	extensible	All Security Labels
Observation.meta.security:TransplantCenter	extensible	All Security Labels
Observation.meta.tag	example	CommonTags
Observation.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding
Observation.status	required	ObservationStatus
Observation.category	preferred	ObservationCategoryCodes
Observation.category:labCategory	preferred	ObservationCategoryCodes
Observation.code	example	Pattern: LOINC code 84413-4
Observation.value[x]	example
Observation.value[x]:valueCodeableConcept	example
Observation.dataAbsentReason	extensible	DataAbsentReason
Observation.interpretation	extensible	ObservationInterpretationCodes
Observation.bodySite	example	SNOMEDCTBodyStructures
Observation.method	example	ObservationMethods
Observation.referenceRange.type	preferred	ObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesTo	example	ObservationReferenceRangeAppliesToCodes
Observation.component.code	example	LOINCCodes (a valid code from LOINC)
Observation.component.dataAbsentReason	extensible	DataAbsentReason
Observation.component.interpretation	extensible	ObservationInterpretationCodes
Observation.component:conclusion-string.code	example	Pattern: conclusion-string
Observation.component:conclusion-string.dataAbsentReason	extensible	DataAbsentReason
Observation.component:conclusion-string.interpretation	extensible	ObservationInterpretationCodes
Observation.component:gene-studied.code	example	Pattern: LOINC code 48018-6
Observation.component:gene-studied.value[x]	required	​Pattern: HGNC:4948("HLA-DRB1")
Observation.component:gene-studied.dataAbsentReason	extensible	DataAbsentReason
Observation.component:gene-studied.interpretation	extensible	ObservationInterpretationCodes
Observation.component:cytogenetic-location.code	example	Pattern: LOINC code 48001-2
Observation.component:cytogenetic-location.dataAbsentReason	extensible	DataAbsentReason
Observation.component:cytogenetic-location.interpretation	extensible	ObservationInterpretationCodes
Observation.component:reference-sequence-assembly.code	example	Pattern: LOINC code 62374-4
Observation.component:reference-sequence-assembly.value[x]	extensible	LOINC LL1040-6
Observation.component:reference-sequence-assembly.dataAbsentReason	extensible	DataAbsentReason
Observation.component:reference-sequence-assembly.interpretation	extensible	ObservationInterpretationCodes

Constraints

Id	Grade	Path(s)	Details	Requirements
GLSC	warning	Observation.value[x]:valueCodeableConcept.coding:GL.code	Use GL String Code to report HLA genotype : matches('^hla#.+')
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()
obs-3	error	Observation.referenceRange	Must have at least a low or a high or text : low.exists() or high.exists() or text.exists()

This structure is derived from HLAGenotype

Summary

Mandatory: 1 element