GO_FHIR - Local Development build (v0.2.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

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Resource Profile: Variant Implication

Base profile that defines characteristics shared by all Variant Implication observations returned from GenomOncology's API suite.

Usage:

• This Resource Profile is not used by any profiles in this Implementation Guide

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 Observation

Name	Flags	Card.	Type	Description & Constraints
Observation		0..*	Observation	Measurements and simple assertions
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
reference-citations		0..*	Reference(Reference Citation)	References URL: http://fhir.genomoncology.io/StructureDefinition/reference-citations
Slices for category		1..*	CodeableConcept	Classification of type of observation Slice: Unordered, Open by value:coding
category:labCategory		1..1	CodeableConcept	Classification of type of observation
coding		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
display		1..1	string	Representation defined by the system Fixed Value: Laboratory
code		1..1	CodeableConcept	Type of observation (code / type) 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://fhir.genomoncology.io/CodeSystem/go-observation-category-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-implication
display		1..1	string	Representation defined by the system Fixed Value: Variant Implication
Slices for component		4..*	BackboneElement	Component results Slice: Unordered, Open by pattern:code
component:variant_description		0..1	BackboneElement	Variant Description
code		1..1	CodeableConcept	variant_description 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant_description
value[x]		0..1	string	Variant description HTML string
component:display		1..1	BackboneElement	Display
code		1..1	CodeableConcept	display 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: display
value[x]		0..1	string	Variant display (mutation string)
component:is_itd		1..1	BackboneElement	Is ITD
code		1..1	CodeableConcept	Is ITD 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: is_itd
value[x]		0..1	boolean	is_ITD
component:mutation_type		0..1	BackboneElement	Mutation Type
code		1..1	CodeableConcept	mutation_type 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: mutation_type
value[x]		0..1	CodeableConcept	Actual component result Binding: GenomOncology Mutation Types (required)
component:tier		1..1	BackboneElement	tier
code		1..1	CodeableConcept	tier 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: tier
value[x]		0..1	CodeableConcept	Actual component result Binding: GenomOncology Variant Tier Values (required)
component:significance		1..1	BackboneElement	significance
code		1..1	CodeableConcept	significance 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: significance
value[x]		0..1	CodeableConcept	Actual component result Binding: GenomOncology Variant Significance (required)
component:potential_germline_findings		0..*	BackboneElement	potential_germline_findings
code		1..1	CodeableConcept	potential_germline_findings 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: potential_germline_findings
value[x]		0..1	string	Potential Germline Findings
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet	URI
Observation.component:mutation_type.value[x]	required	MutationTypeValueSet (a valid code from GenomOncology Mutation Types) http://fhir.genomoncology.io/ValueSet/mutation-type-valueset from this IG
Observation.component:tier.value[x]	required	VariantTierValueSet (a valid code from GenomOncology Variant Tiers) http://fhir.genomoncology.io/ValueSet/variant-tier-valueset from this IG
Observation.component:significance.value[x]	required	VariantSignificanceValueSet (a valid code from GenomOncology Variant Significance) http://fhir.genomoncology.io/ValueSet/variant-significance-valueset from this IG

Name	Flags	Card.	Type	Description & Constraints
Observation	C	0..*	Observation	Measurements and simple assertions dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources dom-3: 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 dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated dom-5: If a resource is contained in another resource, it SHALL NOT have a security label dom-6: A resource should have narrative for robust management obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created ele-1: All FHIR elements must have a @value or children
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
reference-citations		0..*	Reference(Reference Citation)	References URL: http://fhir.genomoncology.io/StructureDefinition/reference-citations ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
status	?!Σ	1..1	code	registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. ele-1: All FHIR elements must have a @value or children
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. ele-1: All FHIR elements must have a @value or children
category:labCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. ele-1: All FHIR elements must have a @value or children
coding	Σ	1..*	Coding	Code defined by a terminology system ele-1: All FHIR elements must have a @value or children 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
display		1..1	string	Representation defined by the system Fixed Value: Laboratory
code	Σ	1..1	CodeableConcept	Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/go-observation-category-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-implication
display		1..1	string	Representation defined by the system Fixed Value: Variant Implication
Slices for component	Σ	4..*	BackboneElement	Component results Slice: Unordered, Open by pattern:code ele-1: All FHIR elements must have a @value or children
component:All Slices				Content/Rules for all slices
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children
component:variant_description	Σ	0..1	BackboneElement	Variant Description ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	variant_description Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant_description
value[x]	Σ	0..1	string	Variant description HTML string ele-1: All FHIR elements must have a @value or children
component:display	Σ	1..1	BackboneElement	Display ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	display Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: display
value[x]	Σ	0..1	string	Variant display (mutation string) ele-1: All FHIR elements must have a @value or children
component:is_itd	Σ	1..1	BackboneElement	Is ITD ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	Is ITD Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: is_itd
value[x]	Σ	0..1	boolean	is_ITD ele-1: All FHIR elements must have a @value or children
component:mutation_type	Σ	0..1	BackboneElement	Mutation Type ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	mutation_type Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: mutation_type
value[x]	Σ	0..1	CodeableConcept	Actual component result Binding: GenomOncology Mutation Types (required) ele-1: All FHIR elements must have a @value or children
component:tier	Σ	1..1	BackboneElement	tier ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	tier Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: tier
value[x]	Σ	0..1	CodeableConcept	Actual component result Binding: GenomOncology Variant Tier Values (required) ele-1: All FHIR elements must have a @value or children
component:significance	Σ	1..1	BackboneElement	significance ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	significance Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: significance
value[x]	Σ	0..1	CodeableConcept	Actual component result Binding: GenomOncology Variant Significance (required) ele-1: All FHIR elements must have a @value or children
component:potential_germline_findings	Σ	0..*	BackboneElement	potential_germline_findings ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	potential_germline_findings Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: potential_germline_findings
value[x]	Σ	0..1	string	Potential Germline Findings ele-1: All FHIR elements must have a @value or children
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet / Code	URI
Observation.status	required	ObservationStatus http://hl7.org/fhir/ValueSet/observation-status|4.0.1 from the FHIR Standard
Observation.category	preferred	ObservationCategoryCodes http://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard
Observation.category:labCategory	preferred	ObservationCategoryCodes http://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard
Observation.code	example	Pattern: variant-implication("Variant Implication") http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component.code	example	LOINCCodes (a valid code from LOINC) http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:variant_description.code	example	Pattern: variant_description http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:display.code	example	Pattern: display http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:is_itd.code	example	Pattern: is_itd http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:mutation_type.code	example	Pattern: mutation_type http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:mutation_type.value[x]	required	MutationTypeValueSet (a valid code from GenomOncology Mutation Types) http://fhir.genomoncology.io/ValueSet/mutation-type-valueset from this IG
Observation.component:tier.code	example	Pattern: tier http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:tier.value[x]	required	VariantTierValueSet (a valid code from GenomOncology Variant Tiers) http://fhir.genomoncology.io/ValueSet/variant-tier-valueset from this IG
Observation.component:significance.code	example	Pattern: significance http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:significance.value[x]	required	VariantSignificanceValueSet (a valid code from GenomOncology Variant Significance) http://fhir.genomoncology.io/ValueSet/variant-significance-valueset from this IG
Observation.component:potential_germline_findings.code	example	Pattern: potential_germline_findings http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
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..*	Observation	Measurements and simple assertions obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
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: 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
reference-citations		0..*	Reference(Reference Citation)	References URL: http://fhir.genomoncology.io/StructureDefinition/reference-citations
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		1..1	string	Representation defined by the system Fixed Value: Laboratory
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	Type of observation (code / type) 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://fhir.genomoncology.io/CodeSystem/go-observation-category-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-implication
display		1..1	string	Representation defined by the system Fixed Value: Variant Implication
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)	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
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)	Who is responsible for the observation
value[x]	ΣC	0..1		Actual 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 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..*	Annotation	Comments about the observation
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		0..1	Reference(Specimen)	Specimen used for this observation
device		0..1	Reference(Device | DeviceMetric)	(Measurement) Device
referenceRange	C	0..*	BackboneElement	Provides guide for interpretation obs-3: Must have at least a low or a high or text
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
derivedFrom	Σ	0..*	Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)	Related measurements the observation is made from
Slices for component	Σ	4..*	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:variant_description	Σ	0..1	BackboneElement	Variant Description
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	variant_description 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant_description
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	Variant description HTML string
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:display	Σ	1..1	BackboneElement	Display
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	display 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: display
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	Variant display (mutation string)
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:is_itd	Σ	1..1	BackboneElement	Is ITD
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	Is ITD 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: is_itd
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	boolean	is_ITD
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:mutation_type	Σ	0..1	BackboneElement	Mutation Type
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	mutation_type 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: mutation_type
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	CodeableConcept	Actual component result Binding: GenomOncology Mutation Types (required)
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:tier	Σ	1..1	BackboneElement	tier
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	tier 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: tier
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	CodeableConcept	Actual component result Binding: GenomOncology Variant Tier Values (required)
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:significance	Σ	1..1	BackboneElement	significance
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	significance 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: significance
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	CodeableConcept	Actual component result Binding: GenomOncology Variant Significance (required)
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:potential_germline_findings	Σ	0..*	BackboneElement	potential_germline_findings
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	potential_germline_findings 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: potential_germline_findings
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	Potential Germline Findings
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	URI
Observation.language	preferred	CommonLanguages http://hl7.org/fhir/ValueSet/languages from the FHIR Standard Additional Bindings Purpose AllLanguages Max Binding
Observation.status	required	ObservationStatus http://hl7.org/fhir/ValueSet/observation-status|4.0.1 from the FHIR Standard
Observation.category	preferred	ObservationCategoryCodes http://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard
Observation.category:labCategory	preferred	ObservationCategoryCodes http://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard
Observation.code	example	Pattern: variant-implication("Variant Implication") http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.bodySite	example	SNOMEDCTBodyStructures http://hl7.org/fhir/ValueSet/body-site from the FHIR Standard
Observation.method	example	ObservationMethods http://hl7.org/fhir/ValueSet/observation-methods from the FHIR Standard
Observation.referenceRange.type	preferred	ObservationReferenceRangeMeaningCodes http://hl7.org/fhir/ValueSet/referencerange-meaning from the FHIR Standard
Observation.referenceRange.appliesTo	example	ObservationReferenceRangeAppliesToCodes http://hl7.org/fhir/ValueSet/referencerange-appliesto from the FHIR Standard
Observation.component.code	example	LOINCCodes (a valid code from LOINC) http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:variant_description.code	example	Pattern: variant_description http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:variant_description.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:variant_description.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:display.code	example	Pattern: display http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:display.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:display.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:is_itd.code	example	Pattern: is_itd http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:is_itd.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:is_itd.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:mutation_type.code	example	Pattern: mutation_type http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:mutation_type.value[x]	required	MutationTypeValueSet (a valid code from GenomOncology Mutation Types) http://fhir.genomoncology.io/ValueSet/mutation-type-valueset from this IG
Observation.component:mutation_type.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:mutation_type.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:tier.code	example	Pattern: tier http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:tier.value[x]	required	VariantTierValueSet (a valid code from GenomOncology Variant Tiers) http://fhir.genomoncology.io/ValueSet/variant-tier-valueset from this IG
Observation.component:tier.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:tier.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:significance.code	example	Pattern: significance http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:significance.value[x]	required	VariantSignificanceValueSet (a valid code from GenomOncology Variant Significance) http://fhir.genomoncology.io/ValueSet/variant-significance-valueset from this IG
Observation.component:significance.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:significance.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:potential_germline_findings.code	example	Pattern: potential_germline_findings http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:potential_germline_findings.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:potential_germline_findings.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
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-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	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()

This structure is derived from Observation

Summary

Mandatory: 7 elements

Extensions

This structure refers to these extensions:

• http://fhir.genomoncology.io/StructureDefinition/reference-citations

Slices

This structure defines the following Slices:

• The element 1 is sliced based on the value of Observation.category
• The element 1 is sliced based on the value of Observation.component

Differential View

This structure is derived from Observation

Name	Flags	Card.	Type	Description & Constraints
Observation		0..*	Observation	Measurements and simple assertions
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
reference-citations		0..*	Reference(Reference Citation)	References URL: http://fhir.genomoncology.io/StructureDefinition/reference-citations
Slices for category		1..*	CodeableConcept	Classification of type of observation Slice: Unordered, Open by value:coding
category:labCategory		1..1	CodeableConcept	Classification of type of observation
coding		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
display		1..1	string	Representation defined by the system Fixed Value: Laboratory
code		1..1	CodeableConcept	Type of observation (code / type) 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://fhir.genomoncology.io/CodeSystem/go-observation-category-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-implication
display		1..1	string	Representation defined by the system Fixed Value: Variant Implication
Slices for component		4..*	BackboneElement	Component results Slice: Unordered, Open by pattern:code
component:variant_description		0..1	BackboneElement	Variant Description
code		1..1	CodeableConcept	variant_description 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant_description
value[x]		0..1	string	Variant description HTML string
component:display		1..1	BackboneElement	Display
code		1..1	CodeableConcept	display 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: display
value[x]		0..1	string	Variant display (mutation string)
component:is_itd		1..1	BackboneElement	Is ITD
code		1..1	CodeableConcept	Is ITD 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: is_itd
value[x]		0..1	boolean	is_ITD
component:mutation_type		0..1	BackboneElement	Mutation Type
code		1..1	CodeableConcept	mutation_type 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: mutation_type
value[x]		0..1	CodeableConcept	Actual component result Binding: GenomOncology Mutation Types (required)
component:tier		1..1	BackboneElement	tier
code		1..1	CodeableConcept	tier 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: tier
value[x]		0..1	CodeableConcept	Actual component result Binding: GenomOncology Variant Tier Values (required)
component:significance		1..1	BackboneElement	significance
code		1..1	CodeableConcept	significance 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: significance
value[x]		0..1	CodeableConcept	Actual component result Binding: GenomOncology Variant Significance (required)
component:potential_germline_findings		0..*	BackboneElement	potential_germline_findings
code		1..1	CodeableConcept	potential_germline_findings 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: potential_germline_findings
value[x]		0..1	string	Potential Germline Findings
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet	URI
Observation.component:mutation_type.value[x]	required	MutationTypeValueSet (a valid code from GenomOncology Mutation Types) http://fhir.genomoncology.io/ValueSet/mutation-type-valueset from this IG
Observation.component:tier.value[x]	required	VariantTierValueSet (a valid code from GenomOncology Variant Tiers) http://fhir.genomoncology.io/ValueSet/variant-tier-valueset from this IG
Observation.component:significance.value[x]	required	VariantSignificanceValueSet (a valid code from GenomOncology Variant Significance) http://fhir.genomoncology.io/ValueSet/variant-significance-valueset from this IG

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
Observation	C	0..*	Observation	Measurements and simple assertions dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources dom-3: 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 dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated dom-5: If a resource is contained in another resource, it SHALL NOT have a security label dom-6: A resource should have narrative for robust management obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created ele-1: All FHIR elements must have a @value or children
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
reference-citations		0..*	Reference(Reference Citation)	References URL: http://fhir.genomoncology.io/StructureDefinition/reference-citations ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
status	?!Σ	1..1	code	registered | preliminary | final | amended + Binding: ObservationStatus (required): Codes providing the status of an observation. ele-1: All FHIR elements must have a @value or children
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. ele-1: All FHIR elements must have a @value or children
category:labCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. ele-1: All FHIR elements must have a @value or children
coding	Σ	1..*	Coding	Code defined by a terminology system ele-1: All FHIR elements must have a @value or children 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
display		1..1	string	Representation defined by the system Fixed Value: Laboratory
code	Σ	1..1	CodeableConcept	Type of observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/go-observation-category-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-implication
display		1..1	string	Representation defined by the system Fixed Value: Variant Implication
Slices for component	Σ	4..*	BackboneElement	Component results Slice: Unordered, Open by pattern:code ele-1: All FHIR elements must have a @value or children
component:All Slices				Content/Rules for all slices
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children
component:variant_description	Σ	0..1	BackboneElement	Variant Description ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	variant_description Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant_description
value[x]	Σ	0..1	string	Variant description HTML string ele-1: All FHIR elements must have a @value or children
component:display	Σ	1..1	BackboneElement	Display ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	display Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: display
value[x]	Σ	0..1	string	Variant display (mutation string) ele-1: All FHIR elements must have a @value or children
component:is_itd	Σ	1..1	BackboneElement	Is ITD ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	Is ITD Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: is_itd
value[x]	Σ	0..1	boolean	is_ITD ele-1: All FHIR elements must have a @value or children
component:mutation_type	Σ	0..1	BackboneElement	Mutation Type ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	mutation_type Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: mutation_type
value[x]	Σ	0..1	CodeableConcept	Actual component result Binding: GenomOncology Mutation Types (required) ele-1: All FHIR elements must have a @value or children
component:tier	Σ	1..1	BackboneElement	tier ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	tier Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: tier
value[x]	Σ	0..1	CodeableConcept	Actual component result Binding: GenomOncology Variant Tier Values (required) ele-1: All FHIR elements must have a @value or children
component:significance	Σ	1..1	BackboneElement	significance ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	significance Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: significance
value[x]	Σ	0..1	CodeableConcept	Actual component result Binding: GenomOncology Variant Significance (required) ele-1: All FHIR elements must have a @value or children
component:potential_germline_findings	Σ	0..*	BackboneElement	potential_germline_findings ele-1: All FHIR elements must have a @value or children
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
code	Σ	1..1	CodeableConcept	potential_germline_findings Binding: LOINCCodes (example): Codes identifying names of simple observations. ele-1: All FHIR elements must have a @value or children 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
code		1..1	code	Symbol in syntax defined by the system Fixed Value: potential_germline_findings
value[x]	Σ	0..1	string	Potential Germline Findings ele-1: All FHIR elements must have a @value or children
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet / Code	URI
Observation.status	required	ObservationStatus http://hl7.org/fhir/ValueSet/observation-status|4.0.1 from the FHIR Standard
Observation.category	preferred	ObservationCategoryCodes http://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard
Observation.category:labCategory	preferred	ObservationCategoryCodes http://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard
Observation.code	example	Pattern: variant-implication("Variant Implication") http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component.code	example	LOINCCodes (a valid code from LOINC) http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:variant_description.code	example	Pattern: variant_description http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:display.code	example	Pattern: display http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:is_itd.code	example	Pattern: is_itd http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:mutation_type.code	example	Pattern: mutation_type http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:mutation_type.value[x]	required	MutationTypeValueSet (a valid code from GenomOncology Mutation Types) http://fhir.genomoncology.io/ValueSet/mutation-type-valueset from this IG
Observation.component:tier.code	example	Pattern: tier http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:tier.value[x]	required	VariantTierValueSet (a valid code from GenomOncology Variant Tiers) http://fhir.genomoncology.io/ValueSet/variant-tier-valueset from this IG
Observation.component:significance.code	example	Pattern: significance http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:significance.value[x]	required	VariantSignificanceValueSet (a valid code from GenomOncology Variant Significance) http://fhir.genomoncology.io/ValueSet/variant-significance-valueset from this IG
Observation.component:potential_germline_findings.code	example	Pattern: potential_germline_findings http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
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..*	Observation	Measurements and simple assertions obs-6: dataAbsentReason SHALL only be present if Observation.value[x] is not present obs-7: If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present
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: 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
reference-citations		0..*	Reference(Reference Citation)	References URL: http://fhir.genomoncology.io/StructureDefinition/reference-citations
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		1..1	string	Representation defined by the system Fixed Value: Laboratory
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	Type of observation (code / type) 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://fhir.genomoncology.io/CodeSystem/go-observation-category-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-implication
display		1..1	string	Representation defined by the system Fixed Value: Variant Implication
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)	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
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)	Who is responsible for the observation
value[x]	ΣC	0..1		Actual 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 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..*	Annotation	Comments about the observation
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		0..1	Reference(Specimen)	Specimen used for this observation
device		0..1	Reference(Device | DeviceMetric)	(Measurement) Device
referenceRange	C	0..*	BackboneElement	Provides guide for interpretation obs-3: Must have at least a low or a high or text
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
derivedFrom	Σ	0..*	Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)	Related measurements the observation is made from
Slices for component	Σ	4..*	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:variant_description	Σ	0..1	BackboneElement	Variant Description
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	variant_description 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant_description
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	Variant description HTML string
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:display	Σ	1..1	BackboneElement	Display
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	display 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: display
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	Variant display (mutation string)
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:is_itd	Σ	1..1	BackboneElement	Is ITD
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	Is ITD 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: is_itd
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	boolean	is_ITD
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:mutation_type	Σ	0..1	BackboneElement	Mutation Type
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	mutation_type 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: mutation_type
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	CodeableConcept	Actual component result Binding: GenomOncology Mutation Types (required)
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:tier	Σ	1..1	BackboneElement	tier
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	tier 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: tier
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	CodeableConcept	Actual component result Binding: GenomOncology Variant Tier Values (required)
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:significance	Σ	1..1	BackboneElement	significance
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	significance 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: significance
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	CodeableConcept	Actual component result Binding: GenomOncology Variant Significance (required)
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:potential_germline_findings	Σ	0..*	BackboneElement	potential_germline_findings
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	potential_germline_findings 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://fhir.genomoncology.io/CodeSystem/observation-variant-implication-component-codesystem
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: potential_germline_findings
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	Potential Germline Findings
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	URI
Observation.language	preferred	CommonLanguages http://hl7.org/fhir/ValueSet/languages from the FHIR Standard Additional Bindings Purpose AllLanguages Max Binding
Observation.status	required	ObservationStatus http://hl7.org/fhir/ValueSet/observation-status|4.0.1 from the FHIR Standard
Observation.category	preferred	ObservationCategoryCodes http://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard
Observation.category:labCategory	preferred	ObservationCategoryCodes http://hl7.org/fhir/ValueSet/observation-category from the FHIR Standard
Observation.code	example	Pattern: variant-implication("Variant Implication") http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.bodySite	example	SNOMEDCTBodyStructures http://hl7.org/fhir/ValueSet/body-site from the FHIR Standard
Observation.method	example	ObservationMethods http://hl7.org/fhir/ValueSet/observation-methods from the FHIR Standard
Observation.referenceRange.type	preferred	ObservationReferenceRangeMeaningCodes http://hl7.org/fhir/ValueSet/referencerange-meaning from the FHIR Standard
Observation.referenceRange.appliesTo	example	ObservationReferenceRangeAppliesToCodes http://hl7.org/fhir/ValueSet/referencerange-appliesto from the FHIR Standard
Observation.component.code	example	LOINCCodes (a valid code from LOINC) http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:variant_description.code	example	Pattern: variant_description http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:variant_description.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:variant_description.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:display.code	example	Pattern: display http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:display.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:display.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:is_itd.code	example	Pattern: is_itd http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:is_itd.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:is_itd.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:mutation_type.code	example	Pattern: mutation_type http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:mutation_type.value[x]	required	MutationTypeValueSet (a valid code from GenomOncology Mutation Types) http://fhir.genomoncology.io/ValueSet/mutation-type-valueset from this IG
Observation.component:mutation_type.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:mutation_type.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:tier.code	example	Pattern: tier http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:tier.value[x]	required	VariantTierValueSet (a valid code from GenomOncology Variant Tiers) http://fhir.genomoncology.io/ValueSet/variant-tier-valueset from this IG
Observation.component:tier.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:tier.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:significance.code	example	Pattern: significance http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:significance.value[x]	required	VariantSignificanceValueSet (a valid code from GenomOncology Variant Significance) http://fhir.genomoncology.io/ValueSet/variant-significance-valueset from this IG
Observation.component:significance.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:significance.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard
Observation.component:potential_germline_findings.code	example	Pattern: potential_germline_findings http://hl7.org/fhir/ValueSet/observation-codes from the FHIR Standard
Observation.component:potential_germline_findings.dataAbsentReason	extensible	DataAbsentReason http://hl7.org/fhir/ValueSet/data-absent-reason from the FHIR Standard
Observation.component:potential_germline_findings.interpretation	extensible	ObservationInterpretationCodes http://hl7.org/fhir/ValueSet/observation-interpretation from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
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-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	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()

This structure is derived from Observation

Summary

Mandatory: 7 elements

Extensions

This structure refers to these extensions:

• http://fhir.genomoncology.io/StructureDefinition/reference-citations

Slices

This structure defines the following Slices:

• The element 1 is sliced based on the value of Observation.category
• The element 1 is sliced based on the value of Observation.component