HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU Ballot 1

This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v0.9.1: STU 1 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

GeneticVariantFound

 

The official URL for this profile is: 

http://hl7.org/fhir/us/mcode/StructureDefinition/onco-core-GeneticVariantFound

Records an alteration in the most common DNA nucleotide sequence. The term variant can be used to describe an alteration that may be benign, pathogenic, or of unknown significance. The term variant is increasingly being used in place of the term mutation. When reporting 'Genetic Variant Found', at least one element out of the following must be reported: 'Variant Found Identifier', 'Variant Found HGVS Name', and 'Variant Found Description'.

This profile builds on USCoreLaboratoryResultObservationProfile.

This profile was published on Thu Aug 01 00:00:00 EDT 2019 as a active by HL7 International Clinical Interoperability Council.

Summary

Mandatory: 0 element (13 nested mandatory elements)
Must-Support: 6 elements
Fixed Value: 12 elements
Prohibited: 13 elements

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element Observation.identifier is sliced based on the value of value:type.coding.code
  • The element Observation.category.coding is sliced based on the value of value:code
  • The element Observation.code.coding is sliced based on the value of value:code
  • The element Observation.component is sliced based on the value of value:code.coding.code
  • The element Observation.component.code.coding is sliced based on the value of value:code

Mapping Source

This structure represents the following mapping definition:

onco.core.GeneticVariantFound maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab:
  Language maps to language
  ImplicitRules maps to implicitRules
  Metadata.VersionId maps to meta.versionId
  Metadata.SourceSystem maps to meta.source
  Metadata.Profile maps to meta.profile
  Metadata.LastUpdated maps to meta.lastUpdated
  Metadata.SecurityLabel maps to meta.security
  Metadata.Tag maps to meta.tag
  Narrative maps to text
  Identifier maps to identifier (slice on = type.coding.code; slice strategy = includes)
  ObservationBasedOn maps to basedOn
  ObservationPartOf maps to partOf
  Status maps to status
  Category maps to category
  Code maps to code
  ObservationSubjectOfRecord maps to subject
  FocalSubject maps to focus
  CareContext maps to encounter
  RelevantTime maps to effective[x] // Add Types Timing, instant
  StatementDateTime maps to issued
  LaboratoryObservationPerformer maps to performer // Added Target Types PractitionerRole, CareTeam
  DataValue maps to value[x] // Add Type integer, remove Type Attachment
  DataAbsentReason maps to dataAbsentReason
  Interpretation maps to interpretation
  Annotation maps to note
  BodyLocation.Code maps to bodySite
  BodyLocation.Laterality maps to bodySite.extension
  BodyLocation.AnatomicalOrientation maps to bodySite.extension
  BodyLocation.RelationToLandmark maps to bodySite.extension
  Method maps to method
  Specimen maps to specimen
  Device maps to device
  ReferenceRange maps to referenceRange
  ReferenceRange.LowerBound maps to referenceRange.low
  ReferenceRange.UpperBound maps to referenceRange.high
  ReferenceRange.Type maps to referenceRange.type
  ReferenceRange.ApplicableSubpopulation maps to referenceRange.appliesTo
  ReferenceRange.ApplicableAgeRange maps to referenceRange.age
  ReferenceRange.Text maps to referenceRange.text
  PanelMembers.Observation maps to hasMember (slice on = $this.resolve().code.coding.code; slice strategy = includes)
  ObservationDerivedFrom maps to derivedFrom
  Components.ObservationComponent maps to component (slice on = code.coding.code; slice strategy = includes)
  Components.ObservationComponent.Code maps to component.code
  Components.ObservationComponent.DataValue maps to component.value[x]
  Components.ObservationComponent.DataAbsentReason maps to component.dataAbsentReason
  Components.ObservationComponent.Interpretation maps to component.interpretation
  Components.ObservationComponent.ReferenceRange maps to component.referenceRange
  Components.ObservationComponent.ReferenceRange.LowerBound maps to component.referenceRange.low
  Components.ObservationComponent.ReferenceRange.UpperBound maps to component.referenceRange.high
  Components.ObservationComponent.ReferenceRange.Type maps to component.referenceRange.type
  Components.ObservationComponent.ReferenceRange.ApplicableSubpopulation maps to component.referenceRange.appliesTo
  Components.ObservationComponent.ReferenceRange.ApplicableAgeRange maps to component.referenceRange.age
  Components.ObservationComponent.ReferenceRange.Text maps to component.referenceRange.text
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation onco-core-GeneticVariantFound
... identifier Slice: Unordered, Open by value:type.coding.code
... identifier 0..1AccessionIdentifier: Identifier assigned by the lab
... identifier 0..1FillerOrderNumber: Identifier assigned by the lab carrying out the test
... identifier 0..1PlacerOrderNumber: Identifier assigned by the requester of the lab
... basedOn Reference(US Core MedicationRequest Profile | ServiceRequest)
... partOf Reference(MedicationAdministration | obf-MedicationStatement | obf-Procedure)A larger event of which this particular Observation is a component or step. For example, an observation as part of a procedure.
... category 1..1
.... coding Slice: Unordered, Open by value:code
.... coding Σ1..1CodingCode defined by a terminology system
..... system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... code Fixed Value: laboratory
... code
.... coding Slice: Unordered, Open by value:code
.... coding Σ1..1CodingGenetic variant assessment
..... system Fixed Value: http://loinc.org
..... code Fixed Value: 69548-6
... subject Reference(obf-Patient)The subject of an observation
... encounter Reference(US Core Encounter Profile)
... performer Reference(US Core Practitioner Profile | US Core Organization Profile)The practitioner that carried out the observation or action
... value[x] 0..0
... dataAbsentReason 0..0
... interpretation 0..1
... bodySite 0..0
... method SBinding: GeneticTestMethodVS (extensible)
... device Reference(US Core Device Profile)
... referenceRange 0..0
... hasMember 0..0
... derivedFrom Reference(US Core DocumentReference Profile | Media | QuestionnaireResponse | obf-Observation)
... component SSlice: Unordered, Open by value:code.coding.code
.... value[x] Quantity, CodeableConcept, string, Range, Ratio, SampledData, time, dateTime, Period
.... referenceRange
..... type Binding: ObservationReferenceRangeMeaningCodes (extensible)
..... appliesTo Binding: ObservationReferenceRangeAppliesToCodes (extensible)
... component S0..1GenomicSourceClass: The genomic class of the specimen being analyzed, for example, germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome
.... code
..... coding Slice: Unordered, Open by value:code
..... coding Σ1..1CodingGenomic source class [Type]
...... system Fixed Value: http://loinc.org
...... code Fixed Value: 48002-0
.... valueCodeableConcept CodeableConceptBinding: GenomicSourceClassVS (required)
.... dataAbsentReason 0..0
.... interpretation 0..1
.... referenceRange 0..0
... component S0..1VariantFoundIdentifier: The variation ID assigned by HGVS, for example, 360448 is the identifier for NM_005228.4(EGFR):c.-237A>G (single nucleotide variant in EGFR)
.... code
..... coding Slice: Unordered, Open by value:code
..... coding Σ1..1CodingDNA sequence variation identifier [Identifier]
...... system Fixed Value: http://loinc.org
...... code Fixed Value: 48003-8
.... valueCodeableConcept CodeableConceptBinding: ClinVarVS (extensible)
.... dataAbsentReason 0..0
.... interpretation 0..1
.... referenceRange 0..0
... component S0..*VariantFoundHGVSName: Symbolic representation of the variant used in HGVS, for example, NM_005228.4(EGFR):c.-237A>G for HVGS variation ID 360448
.... code
..... coding Slice: Unordered, Open by value:code
..... coding Σ1..1CodingGenomic structural variant name
...... system Fixed Value: http://loinc.org
...... code Fixed Value: 82154-6
.... valueString string
.... dataAbsentReason 0..0
.... referenceRange 0..0
... component S0..1VariantFoundDescription: Description of the variant. Ideally, this should be a human-readable 'thumbnail' display.
.... code
..... coding Slice: Unordered, Open by value:code
..... coding Σ1..1CodingDNA sequence variation display name [Text] Narrative
...... system Fixed Value: http://loinc.org
...... code Fixed Value: 47998-0
.... valueString string
.... dataAbsentReason 0..0
.... interpretation 0..1
.... referenceRange 0..0

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*onco-core-GeneticVariantFound
us-core-2: If there is no component or related element then either a value[x] or a data absent reason must be present
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier ΣIdentifierBusiness Identifier for observation
Slice: Unordered, Open by value:type.coding.code
... identifier Σ0..1IdentifierAccessionIdentifier: Identifier assigned by the lab
... identifier Σ0..1IdentifierFillerOrderNumber: Identifier assigned by the lab carrying out the test
... identifier Σ0..1IdentifierPlacerOrderNumber: Identifier assigned by the requester of the lab
... basedOn Σ0..*Reference(US Core MedicationRequest Profile | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | obf-MedicationStatement | obf-Procedure)A larger event of which this particular Observation is a component or step. For example, an observation as part of a procedure.
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category SCodeableConceptClassification of type of observation
Slice: Unordered, Open by pattern:$this
Binding: ObservationCategoryCodes (preferred)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
.... coding Σ1..1CodingCode defined by a terminology system
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... version Σ0..1stringVersion of the system - if relevant
..... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
..... display Σ0..1stringRepresentation defined by the system
..... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text Σ0..1stringPlain text representation of the concept
... category S1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred)

Required Pattern: {"coding":[{"system":"http://terminology.hl7.org/CodeSystem/observation-category","code":"laboratory"}]}
... code SΣ1..1CodeableConceptLaboratory Test Name
Binding: LOINCCodes (extensible)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
.... coding Σ1..1CodingGenetic variant assessment
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... version Σ0..1stringVersion of the system - if relevant
..... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: 69548-6
..... display Σ0..1stringRepresentation defined by the system
..... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text Σ0..1stringPlain text representation of the concept
... subject SΣ1..1Reference(obf-Patient)The subject of an observation
... focus Σ0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(US Core Encounter Profile)Healthcare event during which this observation is made
... effective[x] SΣI0..1dateTime, PeriodClinically relevant time/time-period for observation
us-core-1: Datetime must be at least to day.
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..*Reference(US Core Practitioner Profile | US Core Organization Profile)The practitioner that carried out the observation or action
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
... note 0..*AnnotationComments about the observation
... method S0..1CodeableConceptHow it was done
Binding: GeneticTestMethodVS (extensible)
... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(US Core Device Profile)(Measurement) Device
... derivedFrom Σ0..*Reference(US Core DocumentReference Profile | Media | QuestionnaireResponse | obf-Observation)Related measurements the observation is made from
... component SΣIBackboneElementComponent results
Slice: Unordered, Open by value:code.coding.code
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
.... value[x] Σ0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
.... referenceRange 0..*BackboneElementProvides guide for interpretation of component result
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... low I0..1SimpleQuantityLow Range, if relevant
..... high I0..1SimpleQuantityHigh Range, if relevant
..... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (extensible)
..... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (extensible)
..... age 0..1RangeApplicable age range, if relevant
..... text 0..1stringText based reference range in an observation
... component SΣI0..1BackboneElementGenomicSourceClass: The genomic class of the specimen being analyzed, for example, germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
..... coding Σ1..1CodingGenomic source class [Type]
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... version Σ0..1stringVersion of the system - if relevant
...... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: 48002-0
...... display Σ0..1stringRepresentation defined by the system
...... userSelected Σ0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
.... valueCodeableConcept Σ0..1CodeableConceptActual component result
Binding: GenomicSourceClassVS (required)
.... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
... component SΣI0..1BackboneElementVariantFoundIdentifier: The variation ID assigned by HGVS, for example, 360448 is the identifier for NM_005228.4(EGFR):c.-237A>G (single nucleotide variant in EGFR)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
..... coding Σ1..1CodingDNA sequence variation identifier [Identifier]
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... version Σ0..1stringVersion of the system - if relevant
...... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: 48003-8
...... display Σ0..1stringRepresentation defined by the system
...... userSelected Σ0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
.... valueCodeableConcept Σ0..1CodeableConceptActual component result
Binding: ClinVarVS (extensible)
.... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
... component SΣI0..*BackboneElementVariantFoundHGVSName: Symbolic representation of the variant used in HGVS, for example, NM_005228.4(EGFR):c.-237A>G for HVGS variation ID 360448
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
..... coding Σ1..1CodingGenomic structural variant name
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... version Σ0..1stringVersion of the system - if relevant
...... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: 82154-6
...... display Σ0..1stringRepresentation defined by the system
...... userSelected Σ0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
.... valueString Σ0..1stringActual component result
.... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
... component SΣI0..1BackboneElementVariantFoundDescription: Description of the variant. Ideally, this should be a human-readable 'thumbnail' display.
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
..... coding Σ1..1CodingDNA sequence variation display name [Text] Narrative
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... version Σ0..1stringVersion of the system - if relevant
...... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: 47998-0
...... display Σ0..1stringRepresentation defined by the system
...... userSelected Σ0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
.... valueString Σ0..1stringActual component result
.... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)

doco Documentation for this format

Summary

Mandatory: 0 element (13 nested mandatory elements)
Must-Support: 6 elements
Fixed Value: 12 elements
Prohibited: 13 elements

Structures

This structure refers to these other structures:

Slices

This structure defines the following Slices:

  • The element Observation.identifier is sliced based on the value of value:type.coding.code
  • The element Observation.category.coding is sliced based on the value of value:code
  • The element Observation.code.coding is sliced based on the value of value:code
  • The element Observation.component is sliced based on the value of value:code.coding.code
  • The element Observation.component.code.coding is sliced based on the value of value:code

Mapping Source

This structure represents the following mapping definition:

onco.core.GeneticVariantFound maps to http://hl7.org/fhir/us/core/StructureDefinition/us-core-observation-lab:
  Language maps to language
  ImplicitRules maps to implicitRules
  Metadata.VersionId maps to meta.versionId
  Metadata.SourceSystem maps to meta.source
  Metadata.Profile maps to meta.profile
  Metadata.LastUpdated maps to meta.lastUpdated
  Metadata.SecurityLabel maps to meta.security
  Metadata.Tag maps to meta.tag
  Narrative maps to text
  Identifier maps to identifier (slice on = type.coding.code; slice strategy = includes)
  ObservationBasedOn maps to basedOn
  ObservationPartOf maps to partOf
  Status maps to status
  Category maps to category
  Code maps to code
  ObservationSubjectOfRecord maps to subject
  FocalSubject maps to focus
  CareContext maps to encounter
  RelevantTime maps to effective[x] // Add Types Timing, instant
  StatementDateTime maps to issued
  LaboratoryObservationPerformer maps to performer // Added Target Types PractitionerRole, CareTeam
  DataValue maps to value[x] // Add Type integer, remove Type Attachment
  DataAbsentReason maps to dataAbsentReason
  Interpretation maps to interpretation
  Annotation maps to note
  BodyLocation.Code maps to bodySite
  BodyLocation.Laterality maps to bodySite.extension
  BodyLocation.AnatomicalOrientation maps to bodySite.extension
  BodyLocation.RelationToLandmark maps to bodySite.extension
  Method maps to method
  Specimen maps to specimen
  Device maps to device
  ReferenceRange maps to referenceRange
  ReferenceRange.LowerBound maps to referenceRange.low
  ReferenceRange.UpperBound maps to referenceRange.high
  ReferenceRange.Type maps to referenceRange.type
  ReferenceRange.ApplicableSubpopulation maps to referenceRange.appliesTo
  ReferenceRange.ApplicableAgeRange maps to referenceRange.age
  ReferenceRange.Text maps to referenceRange.text
  PanelMembers.Observation maps to hasMember (slice on = $this.resolve().code.coding.code; slice strategy = includes)
  ObservationDerivedFrom maps to derivedFrom
  Components.ObservationComponent maps to component (slice on = code.coding.code; slice strategy = includes)
  Components.ObservationComponent.Code maps to component.code
  Components.ObservationComponent.DataValue maps to component.value[x]
  Components.ObservationComponent.DataAbsentReason maps to component.dataAbsentReason
  Components.ObservationComponent.Interpretation maps to component.interpretation
  Components.ObservationComponent.ReferenceRange maps to component.referenceRange
  Components.ObservationComponent.ReferenceRange.LowerBound maps to component.referenceRange.low
  Components.ObservationComponent.ReferenceRange.UpperBound maps to component.referenceRange.high
  Components.ObservationComponent.ReferenceRange.Type maps to component.referenceRange.type
  Components.ObservationComponent.ReferenceRange.ApplicableSubpopulation maps to component.referenceRange.appliesTo
  Components.ObservationComponent.ReferenceRange.ApplicableAgeRange maps to component.referenceRange.age
  Components.ObservationComponent.ReferenceRange.Text maps to component.referenceRange.text

Differential View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation onco-core-GeneticVariantFound
... identifier Slice: Unordered, Open by value:type.coding.code
... identifier 0..1AccessionIdentifier: Identifier assigned by the lab
... identifier 0..1FillerOrderNumber: Identifier assigned by the lab carrying out the test
... identifier 0..1PlacerOrderNumber: Identifier assigned by the requester of the lab
... basedOn Reference(US Core MedicationRequest Profile | ServiceRequest)
... partOf Reference(MedicationAdministration | obf-MedicationStatement | obf-Procedure)A larger event of which this particular Observation is a component or step. For example, an observation as part of a procedure.
... category 1..1
.... coding Slice: Unordered, Open by value:code
.... coding Σ1..1CodingCode defined by a terminology system
..... system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... code Fixed Value: laboratory
... code
.... coding Slice: Unordered, Open by value:code
.... coding Σ1..1CodingGenetic variant assessment
..... system Fixed Value: http://loinc.org
..... code Fixed Value: 69548-6
... subject Reference(obf-Patient)The subject of an observation
... encounter Reference(US Core Encounter Profile)
... performer Reference(US Core Practitioner Profile | US Core Organization Profile)The practitioner that carried out the observation or action
... value[x] 0..0
... dataAbsentReason 0..0
... interpretation 0..1
... bodySite 0..0
... method SBinding: GeneticTestMethodVS (extensible)
... device Reference(US Core Device Profile)
... referenceRange 0..0
... hasMember 0..0
... derivedFrom Reference(US Core DocumentReference Profile | Media | QuestionnaireResponse | obf-Observation)
... component SSlice: Unordered, Open by value:code.coding.code
.... value[x] Quantity, CodeableConcept, string, Range, Ratio, SampledData, time, dateTime, Period
.... referenceRange
..... type Binding: ObservationReferenceRangeMeaningCodes (extensible)
..... appliesTo Binding: ObservationReferenceRangeAppliesToCodes (extensible)
... component S0..1GenomicSourceClass: The genomic class of the specimen being analyzed, for example, germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome
.... code
..... coding Slice: Unordered, Open by value:code
..... coding Σ1..1CodingGenomic source class [Type]
...... system Fixed Value: http://loinc.org
...... code Fixed Value: 48002-0
.... valueCodeableConcept CodeableConceptBinding: GenomicSourceClassVS (required)
.... dataAbsentReason 0..0
.... interpretation 0..1
.... referenceRange 0..0
... component S0..1VariantFoundIdentifier: The variation ID assigned by HGVS, for example, 360448 is the identifier for NM_005228.4(EGFR):c.-237A>G (single nucleotide variant in EGFR)
.... code
..... coding Slice: Unordered, Open by value:code
..... coding Σ1..1CodingDNA sequence variation identifier [Identifier]
...... system Fixed Value: http://loinc.org
...... code Fixed Value: 48003-8
.... valueCodeableConcept CodeableConceptBinding: ClinVarVS (extensible)
.... dataAbsentReason 0..0
.... interpretation 0..1
.... referenceRange 0..0
... component S0..*VariantFoundHGVSName: Symbolic representation of the variant used in HGVS, for example, NM_005228.4(EGFR):c.-237A>G for HVGS variation ID 360448
.... code
..... coding Slice: Unordered, Open by value:code
..... coding Σ1..1CodingGenomic structural variant name
...... system Fixed Value: http://loinc.org
...... code Fixed Value: 82154-6
.... valueString string
.... dataAbsentReason 0..0
.... referenceRange 0..0
... component S0..1VariantFoundDescription: Description of the variant. Ideally, this should be a human-readable 'thumbnail' display.
.... code
..... coding Slice: Unordered, Open by value:code
..... coding Σ1..1CodingDNA sequence variation display name [Text] Narrative
...... system Fixed Value: http://loinc.org
...... code Fixed Value: 47998-0
.... valueString string
.... dataAbsentReason 0..0
.... interpretation 0..1
.... referenceRange 0..0

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*onco-core-GeneticVariantFound
us-core-2: If there is no component or related element then either a value[x] or a data absent reason must be present
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier ΣIdentifierBusiness Identifier for observation
Slice: Unordered, Open by value:type.coding.code
... identifier Σ0..1IdentifierAccessionIdentifier: Identifier assigned by the lab
... identifier Σ0..1IdentifierFillerOrderNumber: Identifier assigned by the lab carrying out the test
... identifier Σ0..1IdentifierPlacerOrderNumber: Identifier assigned by the requester of the lab
... basedOn Σ0..*Reference(US Core MedicationRequest Profile | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | obf-MedicationStatement | obf-Procedure)A larger event of which this particular Observation is a component or step. For example, an observation as part of a procedure.
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category SCodeableConceptClassification of type of observation
Slice: Unordered, Open by pattern:$this
Binding: ObservationCategoryCodes (preferred)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
.... coding Σ1..1CodingCode defined by a terminology system
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... version Σ0..1stringVersion of the system - if relevant
..... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
..... display Σ0..1stringRepresentation defined by the system
..... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text Σ0..1stringPlain text representation of the concept
... category S1..1CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred)

Required Pattern: {"coding":[{"system":"http://terminology.hl7.org/CodeSystem/observation-category","code":"laboratory"}]}
... code SΣ1..1CodeableConceptLaboratory Test Name
Binding: LOINCCodes (extensible)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
.... coding Σ1..1CodingGenetic variant assessment
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... version Σ0..1stringVersion of the system - if relevant
..... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: 69548-6
..... display Σ0..1stringRepresentation defined by the system
..... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text Σ0..1stringPlain text representation of the concept
... subject SΣ1..1Reference(obf-Patient)The subject of an observation
... focus Σ0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter Σ0..1Reference(US Core Encounter Profile)Healthcare event during which this observation is made
... effective[x] SΣI0..1dateTime, PeriodClinically relevant time/time-period for observation
us-core-1: Datetime must be at least to day.
... issued Σ0..1instantDate/Time this version was made available
... performer Σ0..*Reference(US Core Practitioner Profile | US Core Organization Profile)The practitioner that carried out the observation or action
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
... note 0..*AnnotationComments about the observation
... method S0..1CodeableConceptHow it was done
Binding: GeneticTestMethodVS (extensible)
... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(US Core Device Profile)(Measurement) Device
... derivedFrom Σ0..*Reference(US Core DocumentReference Profile | Media | QuestionnaireResponse | obf-Observation)Related measurements the observation is made from
... component SΣIBackboneElementComponent results
Slice: Unordered, Open by value:code.coding.code
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
.... value[x] Σ0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
.... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
.... referenceRange 0..*BackboneElementProvides guide for interpretation of component result
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... low I0..1SimpleQuantityLow Range, if relevant
..... high I0..1SimpleQuantityHigh Range, if relevant
..... type 0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (extensible)
..... appliesTo 0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (extensible)
..... age 0..1RangeApplicable age range, if relevant
..... text 0..1stringText based reference range in an observation
... component SΣI0..1BackboneElementGenomicSourceClass: The genomic class of the specimen being analyzed, for example, germline for inherited genome, somatic for cancer genome, and prenatal for fetal genome
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
..... coding Σ1..1CodingGenomic source class [Type]
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... version Σ0..1stringVersion of the system - if relevant
...... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: 48002-0
...... display Σ0..1stringRepresentation defined by the system
...... userSelected Σ0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
.... valueCodeableConcept Σ0..1CodeableConceptActual component result
Binding: GenomicSourceClassVS (required)
.... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
... component SΣI0..1BackboneElementVariantFoundIdentifier: The variation ID assigned by HGVS, for example, 360448 is the identifier for NM_005228.4(EGFR):c.-237A>G (single nucleotide variant in EGFR)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
..... coding Σ1..1CodingDNA sequence variation identifier [Identifier]
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... version Σ0..1stringVersion of the system - if relevant
...... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: 48003-8
...... display Σ0..1stringRepresentation defined by the system
...... userSelected Σ0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
.... valueCodeableConcept Σ0..1CodeableConceptActual component result
Binding: ClinVarVS (extensible)
.... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
... component SΣI0..*BackboneElementVariantFoundHGVSName: Symbolic representation of the variant used in HGVS, for example, NM_005228.4(EGFR):c.-237A>G for HVGS variation ID 360448
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
..... coding Σ1..1CodingGenomic structural variant name
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... version Σ0..1stringVersion of the system - if relevant
...... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: 82154-6
...... display Σ0..1stringRepresentation defined by the system
...... userSelected Σ0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
.... valueString Σ0..1stringActual component result
.... interpretation 0..*CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)
... component SΣI0..1BackboneElementVariantFoundDescription: Description of the variant. Ideally, this should be a human-readable 'thumbnail' display.
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... coding ΣCodingCode defined by a terminology system
Slice: Unordered, Open by value:code
..... coding Σ1..1CodingDNA sequence variation display name [Text] Narrative
...... id 0..1stringUnique id for inter-element referencing
...... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
...... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... version Σ0..1stringVersion of the system - if relevant
...... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: 47998-0
...... display Σ0..1stringRepresentation defined by the system
...... userSelected Σ0..1booleanIf this coding was chosen directly by the user
..... text Σ0..1stringPlain text representation of the concept
.... valueString Σ0..1stringActual component result
.... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretationCodes (extensible)

doco Documentation for this format

Downloads: StructureDefinition: (XML, JSON, TTL), Schema: XML Schematron

 

Terminology Bindings

PathConformanceValueSet / Code
Observation.languagepreferredCommonLanguages
Max Binding: AllLanguages
Observation.statusrequiredObservationStatus
Observation.categorypreferredObservationCategoryCodes
Observation.category:laboratorypreferredPattern: laboratory
Observation.codeextensibleLOINCCodes
Observation.interpretationextensibleObservationInterpretationCodes
Observation.methodextensibleGeneticTestMethodVS
Observation.referenceRange.typeextensibleObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToextensibleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component.interpretationextensibleObservationInterpretationCodes
Observation.component.referenceRange.typeextensibleObservationReferenceRangeMeaningCodes
Observation.component.referenceRange.appliesToextensibleObservationReferenceRangeAppliesToCodes
Observation.component:onco-core-GenomicSourceClass.codeexampleLOINCCodes
Observation.component:onco-core-GenomicSourceClass.valueCodeableConceptrequiredGenomicSourceClassVS
Observation.component:onco-core-GenomicSourceClass.interpretationextensibleObservationInterpretationCodes
Observation.component:onco-core-GenomicSourceClass.referenceRange.typeextensibleObservationReferenceRangeMeaningCodes
Observation.component:onco-core-GenomicSourceClass.referenceRange.appliesToextensibleObservationReferenceRangeAppliesToCodes
Observation.component:onco-core-VariantFoundIdentifier.codeexampleLOINCCodes
Observation.component:onco-core-VariantFoundIdentifier.valueCodeableConceptextensibleClinVarVS
Observation.component:onco-core-VariantFoundIdentifier.interpretationextensibleObservationInterpretationCodes
Observation.component:onco-core-VariantFoundIdentifier.referenceRange.typeextensibleObservationReferenceRangeMeaningCodes
Observation.component:onco-core-VariantFoundIdentifier.referenceRange.appliesToextensibleObservationReferenceRangeAppliesToCodes
Observation.component:onco-core-VariantFoundHGVSName.codeexampleLOINCCodes
Observation.component:onco-core-VariantFoundHGVSName.interpretationextensibleObservationInterpretationCodes
Observation.component:onco-core-VariantFoundHGVSName.referenceRange.typeextensibleObservationReferenceRangeMeaningCodes
Observation.component:onco-core-VariantFoundHGVSName.referenceRange.appliesToextensibleObservationReferenceRangeAppliesToCodes
Observation.component:onco-core-VariantFoundDescription.codeexampleLOINCCodes
Observation.component:onco-core-VariantFoundDescription.interpretationextensibleObservationInterpretationCodes
Observation.component:onco-core-VariantFoundDescription.referenceRange.typeextensibleObservationReferenceRangeMeaningCodes
Observation.component:onco-core-VariantFoundDescription.referenceRange.appliesToextensibleObservationReferenceRangeAppliesToCodes

 

Constraints

IdPathDetailsRequirements
dom-2ObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-4ObservationIf 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-3ObservationIf 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-6ObservationA resource should have narrative for robust management
: text.div.exists()
dom-5ObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
obs-7ObservationIf 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.code = %resource.code.coding.code) and (coding.system = %resource.code.coding.system)).empty()
obs-6ObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.empty()
us-core-2ObservationIf there is no component or related element then either a value[x] or a data absent reason must be present
: (component.empty() and related.empty()) implies (dataAbsentReason or value)
us-core-1Observation.effective[x]Datetime must be at least to day.
: ($this as dateTime).toString().length() >= 8
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())