Haplotype describe a set of genomic variations that appear on a single strand of DNA - and which are therefore typically inherited together. Many haplotypes are expressed as simple strings, and can be conveyed in valueCodeableConcept.text. In some cases, haplotypes are sufficiently standardized to be conveyed as codes in valueCodeableConcept.code.

For Pharmacogenomics, implementers SHOULD send coded haplotypes. Here is an example using PharmVar:

• Coded PGx

  { 
  "valueCodeableConcept": { 
    "coding": [{ 
      "system": "http://www.pharmvar.org", 
      "code": "PV01777", 
      "display": "CYP2C9*3.002" }],
    "text": "CYP2C9*3B" 
    } 
  }
  

For both genotypes and haplotypes, reporting the structured variant data is optional. However, implementers SHOULD when possible. For example, sending PGX star-alleles without variant-level information is not best practice as it is both potentially ambiguous and can preclude future utility of the report.

Review the Genotypes page for guidance on reporting genotypes and haplotypes together.

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

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicFinding	Haplotype Constraints: obs-6, obs-7, obs-8, obs-10, obs-11
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
contained		0..*	Resource	Contained, inline Resources
Slices for extension				Content/Rules for all slices
extension: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: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
extension:body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored
status	?!Σ	1..1	code	registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category		2..*	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		1..1	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: laboratory
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
category:geCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
coding		1..1	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: GE
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
code	ΣC	1..1	CodeableConcept	84414-2 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: 84414-2
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
focus	?!Σ	0..*	Reference(Resource)	What the observation is about, when it is not about the subject of record
value[x]	ΣC	1..1	CodeableConcept	Haplotype name Binding Description: (example): Binding not yet standardized
dataAbsentReason	C	0..1	CodeableConcept	Why the result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
method		0..1	CodeableConcept	Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible)
Slices for derivedFrom	Σ	0..*	Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy)	Related resource from which the observation is made Slice: Unordered, Open by profile:resolve()
derivedFrom:haplotype	Σ	0..*	Reference(Haplotype)	Haplotype this haplotype is derived from
derivedFrom:variant	Σ	0..*	Reference(Variant)	Variant this haplotype is derived from
derivedFrom:molecular-sequence	Σ	0..*	Reference(MolecularSequence)	MolecularSequence this haplotype is derived from
Slices for component	ΣC	0..*	BackboneElement	Component results Slice: Unordered, Open by value:code
component:All Slices				Content/Rules for all slices
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
component:conclusion-string	ΣC	0..1	BackboneElement	Clinical Conclusion
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	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
component:gene-studied	ΣC	0..*	BackboneElement	Gene Studied
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	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]	ΣC	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: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
component:cytogenetic-location	ΣC	0..*	BackboneElement	Cytogenetic (Chromosome) Location
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	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]	ΣC	1..1	CodeableConcept	Example: 1q21.1
component:reference-sequence-assembly	ΣC	0..*	BackboneElement	Human Reference Sequence Assembly
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	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]	ΣC	1..1	CodeableConcept	GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
component:chromosome-identifier	ΣC	0..*	BackboneElement	Chromosome Identifier
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	48000-4 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: 48000-4
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]	ΣC	1..1	CodeableConcept	Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required)
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.status	Base	required	Observation Status	📍6.0.0-ballot3	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.category:geCategory	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.value[x]	Base	example		Not Stated	Unknown
Observation.dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.method	Base	extensible	​ LOINC Answer Codes for LL4050-2 (missing link)	📦	unknown?
Observation.component.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:conclusion-string.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:gene-studied.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:gene-studied.​value[x]	Base	extensible	HUGO Gene Nomenclature Committee Gene Names (HGNC)	📦4.0.0-ballot	This IG
Observation.component:cytogenetic-location.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:reference-sequence-assembly.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:reference-sequence-assembly.​value[x]	Base	extensible	​ LOINC Answer Codes for LL1040-6 (missing link)	📦	unknown?
Observation.component:chromosome-identifier.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:chromosome-identifier.​value[x]	Base	required	​ LOINC Answer Codes for LL2938-0 (missing link)	📦	unknown?

Constraints

Id	Grade	Path(s)	Description	Expression
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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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	Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present	dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value).	value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
obs-8	error	Observation	bodyStructure SHALL only be present if Observation.bodySite is not present	bodySite.exists() implies bodyStructure.empty()
obs-10	error	Observation	Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present	component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
obs-11	error	Observation	if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present	(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())

This structure is derived from GenomicFinding

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation		0..*	GenomicFinding	Haplotype
code		1..1	CodeableConcept	84414-2 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: 84414-2
value[x]		1..1	CodeableConcept	Haplotype name Binding Description: (example): Binding not yet standardized
method		0..1	CodeableConcept	Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible)
Slices for derivedFrom				Content/Rules for all slices
derivedFrom:haplotype		0..*	Reference(Haplotype)	Haplotype this haplotype is derived from
derivedFrom:variant		0..*	Reference(Variant)	Variant this haplotype is derived from
derivedFrom:molecular-sequence		0..*	Reference(MolecularSequence)	MolecularSequence this haplotype is derived from
Documentation for this format

Terminology Bindings (Differential)

Path	Status	Usage	ValueSet	Version	Source
Observation.value[x]	Base	example		Not Stated	Unknown
Observation.method	Base	extensible	​ LOINC Answer Codes for LL4050-2 (missing link)	📦	unknown?

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicFinding	Haplotype Constraints: obs-6, obs-7, obs-8, obs-10, obs-11
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: AllLanguages (required): IETF language tag for a human language Additional Bindings Purpose CommonLanguages Starter
text		0..1	Narrative	Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements
contained		0..*	Resource	Contained, inline Resources
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension: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: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
extension:body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	Business Identifier for observation
instantiates[x]	Σ	0..1	canonical(ObservationDefinition), Reference(ObservationDefinition)	Instantiates FHIR ObservationDefinition
basedOn	Σ	0..*	Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)	Fulfills plan, proposal or order
triggeredBy		0..*	BackboneElement	Triggering observation(s)
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
observation	Σ	1..1	Reference(Observation)	Triggering observation
type	Σ	1..1	code	reflex | repeat | re-run Binding: TriggeredBytype (required): The type of TriggeredBy Observation.
reason		0..1	string	Reason that the observation was triggered
partOf	Σ	0..*	Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | GenomicStudy)	Part of referenced event
status	?!Σ	1..1	code	registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category		2..*	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	id	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
coding		1..1	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: laboratory
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
category:geCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
id		0..1	id	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
coding		1..1	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: GE
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
code	ΣC	1..1	CodeableConcept	84414-2 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: 84414-2
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
subject	Σ	0..1	Reference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct)	Who and/or what the observation is about
focus	?!Σ	0..*	Reference(Resource)	What the observation is about, when it is not about the subject of record
organizer	ΣC	0..1	boolean	This observation organizes/groups a set of sub-observations
encounter	Σ	0..1	Reference(Encounter)	Healthcare event during which this observation is made
effective[x]	Σ	0..1		Clinically relevant time/time-period for observation
effectiveDateTime			dateTime
effectivePeriod			Period
effectiveTiming			Timing
effectiveInstant			instant
issued	Σ	0..1	instant	Date/Time this version was made available
performer	Σ	0..*	Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson | HealthcareService)	Who is responsible for the observation
value[x]	ΣC	1..1	CodeableConcept	Haplotype name Binding Description: (example): Binding not yet standardized
dataAbsentReason	C	0..1	CodeableConcept	Why the result value 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	C	0..1	CodeableConcept	Observed body part Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts
bodyStructure	C	0..1	Reference(BodyStructure)	Observed body structure
method		0..1	CodeableConcept	Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible)
specimen	C	0..1	Reference(Specimen | Group)	Specimen used for this observation Constraints: obs-9
device		0..1	Reference(Device | DeviceMetric)	A reference to the device that generates the measurements or the device settings for the device
referenceRange	C	0..*	BackboneElement	Provides guide for interpretation Constraints: obs-3
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(6.0.0-ballot3)	Low Range, if relevant
high	C	0..1	SimpleQuantity(6.0.0-ballot3)	High Range, if relevant
normalValue		0..1	CodeableConcept	Normal value, if relevant Binding: ObservationReferenceRangeNormalValueCodes (extensible): Codes identifying the normal value of the observation.
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	C	0..1	markdown	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 | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy)	Related resource from which the observation is made Slice: Unordered, Open by profile:resolve()
derivedFrom:haplotype	Σ	0..*	Reference(Haplotype)	Haplotype this haplotype is derived from
derivedFrom:variant	Σ	0..*	Reference(Variant)	Variant this haplotype is derived from
derivedFrom:molecular-sequence	Σ	0..*	Reference(MolecularSequence)	MolecularSequence this haplotype is derived from
Slices for component	ΣC	0..*	BackboneElement	Component results Slice: Unordered, Open by value: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	ΣC	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
value[x]	ΣC	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
valueAttachment			Attachment
valueReference			Reference(MolecularSequence)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value 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 value
component:conclusion-string	ΣC	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	ΣC	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]	ΣC	0..1	string	Summary conclusion (interpretation/impression)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value 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 value
component:gene-studied	ΣC	0..*	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	ΣC	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]	ΣC	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: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value 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 value
component:cytogenetic-location	ΣC	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	ΣC	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]	ΣC	1..1	CodeableConcept	Example: 1q21.1
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value 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 value
component:reference-sequence-assembly	ΣC	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	ΣC	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]	ΣC	1..1	CodeableConcept	GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value 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 value
component:chromosome-identifier	ΣC	0..*	BackboneElement	Chromosome Identifier
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	ΣC	1..1	CodeableConcept	48000-4 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: 48000-4
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]	ΣC	1..1	CodeableConcept	Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value 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 value
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.language	Base	required	All Languages	📍6.0.0-ballot3	FHIR Std.
Observation.triggeredBy.​type	Base	required	triggered Bytype	📍6.0.0-ballot3	FHIR Std.
Observation.status	Base	required	Observation Status	📍6.0.0-ballot3	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.category:geCategory	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.value[x]	Base	example		Not Stated	Unknown
Observation.dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.bodySite	Base	example	SNOMED CT Body Structures	📍6.0.0-ballot3	FHIR Std.
Observation.method	Base	extensible	​ LOINC Answer Codes for LL4050-2 (missing link)	📦	unknown?
Observation.referenceRange.​normalValue	Base	extensible	Observation Reference Range Normal Value Codes	📍6.0.0-ballot3	FHIR Std.
Observation.referenceRange.​type	Base	preferred	Observation Reference Range Meaning Codes	📍6.0.0-ballot3	FHIR Std.
Observation.referenceRange.​appliesTo	Base	example	Observation Reference Range Applies To Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:conclusion-string.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:conclusion-string.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:gene-studied.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:gene-studied.​value[x]	Base	extensible	HUGO Gene Nomenclature Committee Gene Names (HGNC)	📦4.0.0-ballot	This IG
Observation.component:gene-studied.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:gene-studied.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:cytogenetic-location.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:cytogenetic-location.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:reference-sequence-assembly.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:reference-sequence-assembly.​value[x]	Base	extensible	​ LOINC Answer Codes for LL1040-6 (missing link)	📦	unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:chromosome-identifier.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:chromosome-identifier.​value[x]	Base	required	​ LOINC Answer Codes for LL2938-0 (missing link)	📦	unknown?
Observation.component:chromosome-identifier.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:chromosome-identifier.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.

Constraints

Id	Grade	Path(s)	Description	Expression
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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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-3	error	Observation.referenceRange	Must have at least a low or a high or text	low.exists() or high.exists() or text.exists()
obs-6	error	Observation	Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present	dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value).	value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
obs-8	error	Observation	bodyStructure SHALL only be present if Observation.bodySite is not present	bodySite.exists() implies bodyStructure.empty()
obs-9	error	Observation.specimen	If Observation.specimen is a reference to Group, the group can only have specimens	(reference.resolve().exists() and reference.resolve() is Group) implies reference.resolve().member.entity.resolve().all($this is Specimen)
obs-10	error	Observation	Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present	component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
obs-11	error	Observation	if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present	(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())

Key Elements View

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicFinding	Haplotype Constraints: obs-6, obs-7, obs-8, obs-10, obs-11
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
contained		0..*	Resource	Contained, inline Resources
Slices for extension				Content/Rules for all slices
extension: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: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
extension:body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored
status	?!Σ	1..1	code	registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category		2..*	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		1..1	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: laboratory
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
category:geCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
coding		1..1	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: GE
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
code	ΣC	1..1	CodeableConcept	84414-2 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: 84414-2
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
focus	?!Σ	0..*	Reference(Resource)	What the observation is about, when it is not about the subject of record
value[x]	ΣC	1..1	CodeableConcept	Haplotype name Binding Description: (example): Binding not yet standardized
dataAbsentReason	C	0..1	CodeableConcept	Why the result value is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
method		0..1	CodeableConcept	Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible)
Slices for derivedFrom	Σ	0..*	Reference(DocumentReference | ImagingStudy | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy)	Related resource from which the observation is made Slice: Unordered, Open by profile:resolve()
derivedFrom:haplotype	Σ	0..*	Reference(Haplotype)	Haplotype this haplotype is derived from
derivedFrom:variant	Σ	0..*	Reference(Variant)	Variant this haplotype is derived from
derivedFrom:molecular-sequence	Σ	0..*	Reference(MolecularSequence)	MolecularSequence this haplotype is derived from
Slices for component	ΣC	0..*	BackboneElement	Component results Slice: Unordered, Open by value:code
component:All Slices				Content/Rules for all slices
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
component:conclusion-string	ΣC	0..1	BackboneElement	Clinical Conclusion
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	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
component:gene-studied	ΣC	0..*	BackboneElement	Gene Studied
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	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]	ΣC	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: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
component:cytogenetic-location	ΣC	0..*	BackboneElement	Cytogenetic (Chromosome) Location
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	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]	ΣC	1..1	CodeableConcept	Example: 1q21.1
component:reference-sequence-assembly	ΣC	0..*	BackboneElement	Human Reference Sequence Assembly
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	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]	ΣC	1..1	CodeableConcept	GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
component:chromosome-identifier	ΣC	0..*	BackboneElement	Chromosome Identifier
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	ΣC	1..1	CodeableConcept	48000-4 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: 48000-4
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]	ΣC	1..1	CodeableConcept	Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required)
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.status	Base	required	Observation Status	📍6.0.0-ballot3	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.category:geCategory	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.value[x]	Base	example		Not Stated	Unknown
Observation.dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.method	Base	extensible	​ LOINC Answer Codes for LL4050-2 (missing link)	📦	unknown?
Observation.component.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:conclusion-string.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:gene-studied.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:gene-studied.​value[x]	Base	extensible	HUGO Gene Nomenclature Committee Gene Names (HGNC)	📦4.0.0-ballot	This IG
Observation.component:cytogenetic-location.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:reference-sequence-assembly.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:reference-sequence-assembly.​value[x]	Base	extensible	​ LOINC Answer Codes for LL1040-6 (missing link)	📦	unknown?
Observation.component:chromosome-identifier.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:chromosome-identifier.​value[x]	Base	required	​ LOINC Answer Codes for LL2938-0 (missing link)	📦	unknown?

Constraints

Id	Grade	Path(s)	Description	Expression
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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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	Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present	dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value).	value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
obs-8	error	Observation	bodyStructure SHALL only be present if Observation.bodySite is not present	bodySite.exists() implies bodyStructure.empty()
obs-10	error	Observation	Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present	component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
obs-11	error	Observation	if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present	(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())

Differential View

This structure is derived from GenomicFinding

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation		0..*	GenomicFinding	Haplotype
code		1..1	CodeableConcept	84414-2 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: 84414-2
value[x]		1..1	CodeableConcept	Haplotype name Binding Description: (example): Binding not yet standardized
method		0..1	CodeableConcept	Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible)
Slices for derivedFrom				Content/Rules for all slices
derivedFrom:haplotype		0..*	Reference(Haplotype)	Haplotype this haplotype is derived from
derivedFrom:variant		0..*	Reference(Variant)	Variant this haplotype is derived from
derivedFrom:molecular-sequence		0..*	Reference(MolecularSequence)	MolecularSequence this haplotype is derived from
Documentation for this format

Terminology Bindings (Differential)

Path	Status	Usage	ValueSet	Version	Source
Observation.value[x]	Base	example		Not Stated	Unknown
Observation.method	Base	extensible	​ LOINC Answer Codes for LL4050-2 (missing link)	📦	unknown?

Snapshot View

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicFinding	Haplotype Constraints: obs-6, obs-7, obs-8, obs-10, obs-11
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: AllLanguages (required): IETF language tag for a human language Additional Bindings Purpose CommonLanguages Starter
text		0..1	Narrative	Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements
contained		0..*	Resource	Contained, inline Resources
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension: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: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
extension:body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	Business Identifier for observation
instantiates[x]	Σ	0..1	canonical(ObservationDefinition), Reference(ObservationDefinition)	Instantiates FHIR ObservationDefinition
basedOn	Σ	0..*	Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)	Fulfills plan, proposal or order
triggeredBy		0..*	BackboneElement	Triggering observation(s)
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
observation	Σ	1..1	Reference(Observation)	Triggering observation
type	Σ	1..1	code	reflex | repeat | re-run Binding: TriggeredBytype (required): The type of TriggeredBy Observation.
reason		0..1	string	Reason that the observation was triggered
partOf	Σ	0..*	Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy | GenomicStudy)	Part of referenced event
status	?!Σ	1..1	code	registered | specimen-in-process | preliminary | final | amended | corrected | appended | cancelled | entered-in-error | unknown | cannot-be-obtained Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category		2..*	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	id	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
coding		1..1	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: laboratory
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
category:geCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
id		0..1	id	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
coding		1..1	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/v2-0074
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: GE
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
code	ΣC	1..1	CodeableConcept	84414-2 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: 84414-2
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
subject	Σ	0..1	Reference(Patient | Group | Device | Location | Organization | Procedure | Practitioner | Medication | Substance | BiologicallyDerivedProduct | NutritionProduct)	Who and/or what the observation is about
focus	?!Σ	0..*	Reference(Resource)	What the observation is about, when it is not about the subject of record
organizer	ΣC	0..1	boolean	This observation organizes/groups a set of sub-observations
encounter	Σ	0..1	Reference(Encounter)	Healthcare event during which this observation is made
effective[x]	Σ	0..1		Clinically relevant time/time-period for observation
effectiveDateTime			dateTime
effectivePeriod			Period
effectiveTiming			Timing
effectiveInstant			instant
issued	Σ	0..1	instant	Date/Time this version was made available
performer	Σ	0..*	Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson | HealthcareService)	Who is responsible for the observation
value[x]	ΣC	1..1	CodeableConcept	Haplotype name Binding Description: (example): Binding not yet standardized
dataAbsentReason	C	0..1	CodeableConcept	Why the result value 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	C	0..1	CodeableConcept	Observed body part Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts
bodyStructure	C	0..1	Reference(BodyStructure)	Observed body structure
method		0..1	CodeableConcept	Directly measured | Family DNA | Family history | Inferred from population data Binding: LOINC Answer List LL4050-2 (extensible)
specimen	C	0..1	Reference(Specimen | Group)	Specimen used for this observation Constraints: obs-9
device		0..1	Reference(Device | DeviceMetric)	A reference to the device that generates the measurements or the device settings for the device
referenceRange	C	0..*	BackboneElement	Provides guide for interpretation Constraints: obs-3
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(6.0.0-ballot3)	Low Range, if relevant
high	C	0..1	SimpleQuantity(6.0.0-ballot3)	High Range, if relevant
normalValue		0..1	CodeableConcept	Normal value, if relevant Binding: ObservationReferenceRangeNormalValueCodes (extensible): Codes identifying the normal value of the observation.
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	C	0..1	markdown	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 | ImagingSelection | QuestionnaireResponse | Observation | MolecularSequence | GenomicStudy)	Related resource from which the observation is made Slice: Unordered, Open by profile:resolve()
derivedFrom:haplotype	Σ	0..*	Reference(Haplotype)	Haplotype this haplotype is derived from
derivedFrom:variant	Σ	0..*	Reference(Variant)	Variant this haplotype is derived from
derivedFrom:molecular-sequence	Σ	0..*	Reference(MolecularSequence)	MolecularSequence this haplotype is derived from
Slices for component	ΣC	0..*	BackboneElement	Component results Slice: Unordered, Open by value: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	ΣC	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
value[x]	ΣC	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
valueAttachment			Attachment
valueReference			Reference(MolecularSequence)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value 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 value
component:conclusion-string	ΣC	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	ΣC	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]	ΣC	0..1	string	Summary conclusion (interpretation/impression)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value 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 value
component:gene-studied	ΣC	0..*	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	ΣC	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]	ΣC	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: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value 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 value
component:cytogenetic-location	ΣC	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	ΣC	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]	ΣC	1..1	CodeableConcept	Example: 1q21.1
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value 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 value
component:reference-sequence-assembly	ΣC	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	ΣC	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]	ΣC	1..1	CodeableConcept	GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value 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 value
component:chromosome-identifier	ΣC	0..*	BackboneElement	Chromosome Identifier
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	ΣC	1..1	CodeableConcept	48000-4 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: 48000-4
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]	ΣC	1..1	CodeableConcept	Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result value 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 value
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.language	Base	required	All Languages	📍6.0.0-ballot3	FHIR Std.
Observation.triggeredBy.​type	Base	required	triggered Bytype	📍6.0.0-ballot3	FHIR Std.
Observation.status	Base	required	Observation Status	📍6.0.0-ballot3	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.category:geCategory	Base	preferred	Observation Category Codes	📍6.0.0-ballot3	FHIR Std.
Observation.code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.value[x]	Base	example		Not Stated	Unknown
Observation.dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.bodySite	Base	example	SNOMED CT Body Structures	📍6.0.0-ballot3	FHIR Std.
Observation.method	Base	extensible	​ LOINC Answer Codes for LL4050-2 (missing link)	📦	unknown?
Observation.referenceRange.​normalValue	Base	extensible	Observation Reference Range Normal Value Codes	📍6.0.0-ballot3	FHIR Std.
Observation.referenceRange.​type	Base	preferred	Observation Reference Range Meaning Codes	📍6.0.0-ballot3	FHIR Std.
Observation.referenceRange.​appliesTo	Base	example	Observation Reference Range Applies To Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:conclusion-string.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:conclusion-string.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:gene-studied.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:gene-studied.​value[x]	Base	extensible	HUGO Gene Nomenclature Committee Gene Names (HGNC)	📦4.0.0-ballot	This IG
Observation.component:gene-studied.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:gene-studied.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:cytogenetic-location.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:cytogenetic-location.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:reference-sequence-assembly.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:reference-sequence-assembly.​value[x]	Base	extensible	​ LOINC Answer Codes for LL1040-6 (missing link)	📦	unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:chromosome-identifier.​code	Base	example	LOINC Codes	📍6.0.0-ballot3	FHIR Std.
Observation.component:chromosome-identifier.​value[x]	Base	required	​ LOINC Answer Codes for LL2938-0 (missing link)	📦	unknown?
Observation.component:chromosome-identifier.​dataAbsentReason	Base	extensible	Data Absent Reason	📍6.0.0-ballot3	FHIR Std.
Observation.component:chromosome-identifier.​interpretation	Base	extensible	Observation Interpretation Codes	📍6.0.0-ballot3	FHIR Std.

Constraints

Id	Grade	Path(s)	Description	Expression
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.trace('id') in %resource.descendants().select(reference | as(uri))) or descendants().where(reference='#' | as(uri)='#').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-3	error	Observation.referenceRange	Must have at least a low or a high or text	low.exists() or high.exists() or text.exists()
obs-6	error	Observation	Observation.dataAbsentReason SHALL only be present if Observation.value[x] is not present	dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.component.code is the same as Observation.code, then Observation.value SHALL NOT be present (the Observation.component.value[x] holds the value).	value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()
obs-8	error	Observation	bodyStructure SHALL only be present if Observation.bodySite is not present	bodySite.exists() implies bodyStructure.empty()
obs-9	error	Observation.specimen	If Observation.specimen is a reference to Group, the group can only have specimens	(reference.resolve().exists() and reference.resolve() is Group) implies reference.resolve().member.entity.resolve().all($this is Specimen)
obs-10	error	Observation	Observation.component.dataAbsentReason SHALL only be present if Observation.component.value[x] is not present	component.empty() or component.where(dataAbsentReason.exists()).all(value.empty())
obs-11	error	Observation	if organizer exists and organizer = true, then value[x], dataAbsentReason and component SHALL NOT be present	(organizer.exists() and organizer.allTrue()) implies (value.empty() and dataAbsentReason.empty() and component.empty())

This structure is derived from GenomicFinding

Summary

Mandatory: 1 element

Structures

This structure refers to these other structures:

• Haplotype (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/haplotype)
• Variant (http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant)

Maturity: 2