FHIR Release 3 (STU)

This page is part of the FHIR Specification (v3.0.2: STU 3). The current version which supercedes this version is 5.0.0. For a full list of available versions, see the Directory of published versions . Page versions: R4B R4 R3

10.1.14.6 StructureDefinition: Observation-Genetics

(No assigned work group) Maturity Level: 1InformativeUse Context: Any

The official URL for this profile is: 

http://hl7.org/fhir/StructureDefinition/observation-genetics

Describes how the observation resource is used to report structured genetic test results

This profile was published on Mon, Mar 14, 2016 00:00+1100 as a draft by Health Level Seven International (Clinical Genomics).

10.1.14.6.1 Formal Views of Profile Content

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

This structure is derived from Observation.

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*
... observation-geneticsDNASequenceVariantName 0..1CodeableConceptDNA sequence variant
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNASequenceVariantName
Binding: ???? (preferred)
... observation-geneticsDNAVariantId 0..1CodeableConceptDNA sequence variant ID
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNAVariantId
... observation-geneticsDNASequenceVariantType 0..1CodeableConceptDNA sequence variant type
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNASequenceVariantType
... observation-geneticsAminoAcidChangeName 0..1CodeableConceptAmino acid change
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName
Binding: ???? (preferred)
... observation-geneticsAminoAcidChangeType 0..1CodeableConceptAmino Acid Change Type
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeType
... observation-geneticsGene 0..1CodeableConceptHGNC gene symbol
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
Binding: ???? (preferred)
... observation-geneticsDNARegionName 0..1stringDNA region name
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNARegionName
... observation-geneticsAlleleName 0..1CodeableConceptName of allele
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAlleleName
Binding: ???? (preferred)
... observation-geneticsAllelicState 0..1CodeableConceptThe level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAllelicState
... observation-geneticsAllelicFrequency 0..1decimalAllele frequency
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAllelicFrequency
... observation-geneticsCopyNumberEvent 0..1CodeableConceptCopy number variation
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsCopyNumberEvent
... observation-geneticsGenomicSourceClass 0..1CodeableConceptGenomic source class
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsGenomicSourceClass
... observation-geneticsPhaseSet 0..1uriPhase set identifier (UUID/OID)
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsPhaseSet
... observation-geneticsSequence 0..*Reference(Sequence)Sequence
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence
... observation-geneticsInterpretation 0..1Reference(Observation)Clinical interpretations for variant
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsInterpretation

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Measurements and simple assertions
... 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: Common Languages (extensible)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... observation-geneticsDNASequenceVariantName I0..1CodeableConceptDNA sequence variant
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNASequenceVariantName
Binding: ???? (preferred)
... observation-geneticsDNAVariantId I0..1CodeableConceptDNA sequence variant ID
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNAVariantId
... observation-geneticsDNASequenceVariantType I0..1CodeableConceptDNA sequence variant type
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNASequenceVariantType
... observation-geneticsAminoAcidChangeName I0..1CodeableConceptAmino acid change
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName
Binding: ???? (preferred)
... observation-geneticsAminoAcidChangeType I0..1CodeableConceptAmino Acid Change Type
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeType
... observation-geneticsGene I0..1CodeableConceptHGNC gene symbol
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
Binding: ???? (preferred)
... observation-geneticsDNARegionName I0..1stringDNA region name
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNARegionName
... observation-geneticsAlleleName I0..1CodeableConceptName of allele
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAlleleName
Binding: ???? (preferred)
... observation-geneticsAllelicState I0..1CodeableConceptThe level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAllelicState
... observation-geneticsAllelicFrequency I0..1decimalAllele frequency
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAllelicFrequency
... observation-geneticsCopyNumberEvent I0..1CodeableConceptCopy number variation
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsCopyNumberEvent
... observation-geneticsGenomicSourceClass I0..1CodeableConceptGenomic source class
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsGenomicSourceClass
... observation-geneticsPhaseSet I0..1uriPhase set identifier (UUID/OID)
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsPhaseSet
... observation-geneticsSequence I0..*Reference(Sequence)Sequence
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence
... observation-geneticsInterpretation I0..1Reference(Observation)Clinical interpretations for variant
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsInterpretation
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn Σ0..*Reference(CarePlan), Reference(DeviceRequest), Reference(ImmunizationRecommendation), Reference(MedicationRequest), Reference(NutritionOrder), Reference(ProcedureRequest), Reference(ReferralRequest)Fulfills plan, proposal or order
... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category 0..*CodeableConceptClassification of type of observation
Binding: Observation Category Codes (preferred)
... code Σ1..1CodeableConceptType of observation (code / type)
Binding: LOINC Codes (example)
... subject Σ0..1Reference(Patient), Reference(Group), Reference(Device), Reference(Location)Who and/or what this is about
... context 0..1Reference(Encounter), Reference(EpisodeOfCare)Healthcare event during which this observation is made
... effective[x] Σ0..1dateTime, PeriodClinically relevant time/time-period for observation
... issued Σ0..1instantDate/Time this was made available
... performer Σ0..*Reference(Practitioner), Reference(Organization), Reference(Patient), Reference(RelatedPerson)Who is responsible for the observation
... value[x] ΣI0..1Quantity, CodeableConcept, string, boolean, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual result
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: Observation Value Absent Reason (extensible)
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
... comment 0..1stringComments about result
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMED CT Body Structures (example)
... method 0..1CodeableConceptHow it was done
Binding: Observation Methods (example)
... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device), Reference(DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: Observation Reference Range Meaning Codes (extensible)
.... appliesTo 0..*CodeableConceptReference range population
Binding: Observation Reference Range Applies To Codes (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... related ΣI0..*BackboneElementResource related to this observation
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... type 0..1codehas-member | derived-from | sequel-to | replaces | qualified-by | interfered-by
Binding: ObservationRelationshipType (required)
.... target 1..1Reference(Observation), Reference(QuestionnaireResponse), Reference(Sequence)Resource that is related to this one
... component ΣI0..*BackboneElementComponent results
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINC Codes (example)
.... value[x] Σ0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: Observation Value Absent Reason (extensible)
.... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result

doco Documentation for this format
<!-- Observation-genetics -->doco

<Observation xmlns="http://hl7.org/fhir"
>
  <!-- from Element: extension -->
 <id value="[id]"/><!-- 0..1 Logical id of this artifact -->
 <meta><!-- 0..1 Meta Metadata about the resource --></meta>
 <implicitRules value="[uri]"/><!-- 0..1 A set of rules under which this content was created -->
 <language value="[code]"/><!-- 0..1 Language of the resource content  -->
 <text><!-- 0..1 Narrative 
     Text summary of the resource, for human interpretation --></text>
 <contained><!-- 0..* Resource Contained, inline Resources --></contained>
 <modifierExtension><!-- 0..* Extension  Extensions that cannot be ignored  --></modifierExtension>
 <identifier><!-- 0..* Identifier 
     Business Identifier for observation --></identifier>
 <basedOn><!-- 0..* Reference(CarePlan)|Reference(DeviceRequest)|Reference(ImmunizationRecommendation)|Reference(MedicationRequest)|
   Reference(NutritionOrder)|Reference(ProcedureRequest)|Reference(ReferralRequest) Fulfills plan, proposal or order --></basedOn>
 <status value="[code]"/><!-- 1..1 registered | preliminary | final | amended +  -->
 <category><!-- 0..* CodeableConcept Classification of  type of observation  --></category>
 <code><!-- 1..1 CodeableConcept Type of observation (code / type)  --></code>
 <subject><!-- 0..1 Reference(Patient)|Reference(Group)|Reference(Device)|Reference(Location) 
     Who and/or what this is about --></subject>
 <context><!-- 0..1 Reference(Encounter)|Reference(EpisodeOfCare) 
     Healthcare event during which this observation is made --></context>
 <effective[x]><!-- 0..1 dateTime|Period 
     Clinically relevant time/time-period for observation --></effective[x]>
 <issued value="[instant]"/><!-- 0..1 Date/Time this was made available -->
 <performer><!-- 0..* Reference(Practitioner)|Reference(Organization)|Reference(Patient)|Reference(RelatedPerson) 
     Who is responsible for the observation --></performer>
 <value[x]><!-- 0..1 Quantity|CodeableConcept|string|boolean|Range|
   Ratio|SampledData|Attachment|time|dateTime|Period Actual result --></value[x]>
 <dataAbsentReason><!-- 0..1 CodeableConcept Why the result is missing  --></dataAbsentReason>
 <interpretation><!-- 0..1 CodeableConcept High, low, normal, etc.  --></interpretation>
 <comment value="[string]"/><!-- 0..1 Comments about result -->
 <bodySite><!-- 0..1 CodeableConcept Observed body part  --></bodySite>
 <method><!-- 0..1 CodeableConcept How it was done  --></method>
 <specimen><!-- 0..1 Reference(Specimen) Specimen used for this observation --></specimen>
 <device><!-- 0..1 Reference(Device)|Reference(DeviceMetric) (Measurement) Device --></device>
 <referenceRange> ?? 0..* BackboneElement  <!-- ?? 0..* Provides guide for interpretation -->
  <modifierExtension><!-- 0..* Extension  Extensions that cannot be ignored  --></modifierExtension>
  <low><!-- 0..1 Quantity 
      Low Range, if relevant --></low>
  <high><!-- 0..1 Quantity 
      High Range, if relevant --></high>
  <type><!-- 0..1 CodeableConcept Reference range qualifier  --></type>
  <appliesTo><!-- 0..* CodeableConcept Reference range population  --></appliesTo>
  <age><!-- 0..1 Range 
      Applicable age range, if relevant --></age>
  <text value="[string]"/><!-- 0..1 Text based reference range in an observation -->
 </referenceRange>
 <related> ?? 0..* BackboneElement  <!-- ?? 0..* Resource related to this observation -->
  <modifierExtension><!-- 0..* Extension  Extensions that cannot be ignored  --></modifierExtension>
  <type value="[code]"/><!-- 0..1 has-member | derived-from | sequel-to | replaces | qualified-by | interfered-by  -->
  <target><!-- 1..1 Reference(Observation)|Reference(QuestionnaireResponse)|Reference(Sequence) 
      Resource that is related to this one --></target>
 </related>
 <component> ?? 0..* BackboneElement  <!-- ?? 0..* Component results -->
  <modifierExtension><!-- 0..* Extension  Extensions that cannot be ignored  --></modifierExtension>
  <code><!-- 1..1 CodeableConcept Type of component observation (code / type)  --></code>
  <value[x]><!-- 0..1 Quantity|CodeableConcept|string|
    Range|Ratio|SampledData|Attachment|time|dateTime|Period 
      Actual component result --></value[x]>
  <dataAbsentReason><!-- 0..1 CodeableConcept Why the component result is missing  --></dataAbsentReason>
  <interpretation><!-- 0..1 CodeableConcept High, low, normal, etc.  --></interpretation>
  <referenceRange><!-- See #Observation.referenceRange  Provides guide for interpretation of component result --></referenceRange>
 </component>
</Observation>

{ // Observation-genetics
  // from Element: extension
    "meta" : { Meta }, //Metadata about the resource
    "implicitRules" : "<uri>", //A set of rules under which this content was created
    "language" : "<code>", //Language of the resource content 
    "text" : { Narrative }, //Text summary of the resource, for human interpretation
    "contained" : [{ Resource }], //Contained, inline Resources
    "extension" : [ //  sliced by value:url  in the specified orderOpen
      { // DNA sequence variant // C?
        // from Element: extension
      },
      { // DNA sequence variant ID // C?
        // from Element: extension
      },
      { // DNA sequence variant type // C?
        // from Element: extension
      },
      { // Amino acid change // C?
        // from Element: extension
      },
      { // Amino Acid Change Type // C?
        // from Element: extension
      },
      { // HGNC gene symbol // C?
        // from Element: extension
      },
      { // DNA region name // C?
        // from Element: extension
      },
      { // Name of allele // C?
        // from Element: extension
      },
      { // The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous // C?
        // from Element: extension
      },
      { // Allele frequency // C?
        // from Element: extension
      },
      { // Copy number variation // C?
        // from Element: extension
      },
      { // Genomic source class // C?
        // from Element: extension
      },
      { // Phase set identifier (UUID/OID) // C?
        // from Element: extension
      },
      { // Sequence // C?
        // from Element: extension
      },
      { // Clinical interpretations for variant // C?
        // from Element: extension
      }
    ],
    "modifierExtension" : [{ Extension }], //Extensions that cannot be ignored
    "identifier" : [{ Identifier }], //Business Identifier for observation
// value[x]: Fulfills plan, proposal or order. One of these 7:
    "basedOn" : [{ Reference(CarePlan) }], //Fulfills plan, proposal or order
    "basedOn" : [{ Reference(DeviceRequest) }], //Fulfills plan, proposal or order
    "basedOn" : [{ Reference(ImmunizationRecommendation) }], //Fulfills plan, proposal or order
    "basedOn" : [{ Reference(MedicationRequest) }], //Fulfills plan, proposal or order
    "basedOn" : [{ Reference(NutritionOrder) }], //Fulfills plan, proposal or order
    "basedOn" : [{ Reference(ProcedureRequest) }], //Fulfills plan, proposal or order
    "basedOn" : [{ Reference(ReferralRequest) }], //Fulfills plan, proposal or order
    "status" : "<code>", // R! registered | preliminary | final | amended + 
    "category" : [{ CodeableConcept }], //Classification of  type of observation 
    "code" : { CodeableConcept }, // R! Type of observation (code / type) 
// value[x]: Who and/or what this is about. One of these 4:
    "subject" : { Reference(Patient) }, //Who and/or what this is about
    "subject" : { Reference(Group) }, //Who and/or what this is about
    "subject" : { Reference(Device) }, //Who and/or what this is about
    "subject" : { Reference(Location) }, //Who and/or what this is about
// value[x]: Healthcare event during which this observation is made. One of these 2:
    "context" : { Reference(Encounter) }, //Healthcare event during which this observation is made
    "context" : { Reference(EpisodeOfCare) }, //Healthcare event during which this observation is made
// value[x]: Clinically relevant time/time-period for observation. One of these 2:
    "effectiveDateTime" : "<dateTime>", //Clinically relevant time/time-period for observation
    "effectivePeriod" : { Period }, //Clinically relevant time/time-period for observation
    "issued" : "<instant>", //Date/Time this was made available
// value[x]: Who is responsible for the observation. One of these 4:
    "performer" : [{ Reference(Practitioner) }], //Who is responsible for the observation
    "performer" : [{ Reference(Organization) }], //Who is responsible for the observation
    "performer" : [{ Reference(Patient) }], //Who is responsible for the observation
    "performer" : [{ Reference(RelatedPerson) }], //Who is responsible for the observation
// value[x]: Actual result. One of these 11:
    "valueQuantity" : { Quantity }, //Actual result
    "valueCodeableConcept" : { CodeableConcept }, //Actual result
    "valueString" : "<string>", //Actual result
    "valueBoolean" : <boolean>, //Actual result
    "valueRange" : { Range }, //Actual result
    "valueRatio" : { Ratio }, //Actual result
    "valueSampledData" : { SampledData }, //Actual result
    "valueAttachment" : { Attachment }, //Actual result
    "valueTime" : "<time>", //Actual result
    "valueDateTime" : "<dateTime>", //Actual result
    "valuePeriod" : { Period }, //Actual result
    "dataAbsentReason" : { CodeableConcept } //Why the result is missing 
    "interpretation" : { CodeableConcept }, //High, low, normal, etc. 
    "comment" : "<string>", //Comments about result
    "bodySite" : { CodeableConcept }, //Observed body part 
    "method" : { CodeableConcept }, //How it was done 
    "specimen" : { Reference(Specimen) }, //Specimen used for this observation
// value[x]: (Measurement) Device. One of these 2:
    "device" : { Reference(Device) }, //(Measurement) Device
    "device" : { Reference(DeviceMetric) }, //(Measurement) Device
    "referenceRange" : [{ BackboneElement }], // C?Provides guide for interpretation
    "related" : [{ BackboneElement }], // C?Resource related to this observation
    "component" : [{ BackboneElement }], // C?Component results
  }

Differential View

This structure is derived from Observation.

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*
... observation-geneticsDNASequenceVariantName 0..1CodeableConceptDNA sequence variant
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNASequenceVariantName
Binding: ???? (preferred)
... observation-geneticsDNAVariantId 0..1CodeableConceptDNA sequence variant ID
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNAVariantId
... observation-geneticsDNASequenceVariantType 0..1CodeableConceptDNA sequence variant type
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNASequenceVariantType
... observation-geneticsAminoAcidChangeName 0..1CodeableConceptAmino acid change
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName
Binding: ???? (preferred)
... observation-geneticsAminoAcidChangeType 0..1CodeableConceptAmino Acid Change Type
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeType
... observation-geneticsGene 0..1CodeableConceptHGNC gene symbol
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
Binding: ???? (preferred)
... observation-geneticsDNARegionName 0..1stringDNA region name
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNARegionName
... observation-geneticsAlleleName 0..1CodeableConceptName of allele
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAlleleName
Binding: ???? (preferred)
... observation-geneticsAllelicState 0..1CodeableConceptThe level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAllelicState
... observation-geneticsAllelicFrequency 0..1decimalAllele frequency
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAllelicFrequency
... observation-geneticsCopyNumberEvent 0..1CodeableConceptCopy number variation
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsCopyNumberEvent
... observation-geneticsGenomicSourceClass 0..1CodeableConceptGenomic source class
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsGenomicSourceClass
... observation-geneticsPhaseSet 0..1uriPhase set identifier (UUID/OID)
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsPhaseSet
... observation-geneticsSequence 0..*Reference(Sequence)Sequence
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence
... observation-geneticsInterpretation 0..1Reference(Observation)Clinical interpretations for variant
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsInterpretation

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Measurements and simple assertions
... 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: Common Languages (extensible)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... observation-geneticsDNASequenceVariantName I0..1CodeableConceptDNA sequence variant
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNASequenceVariantName
Binding: ???? (preferred)
... observation-geneticsDNAVariantId I0..1CodeableConceptDNA sequence variant ID
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNAVariantId
... observation-geneticsDNASequenceVariantType I0..1CodeableConceptDNA sequence variant type
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNASequenceVariantType
... observation-geneticsAminoAcidChangeName I0..1CodeableConceptAmino acid change
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeName
Binding: ???? (preferred)
... observation-geneticsAminoAcidChangeType I0..1CodeableConceptAmino Acid Change Type
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAminoAcidChangeType
... observation-geneticsGene I0..1CodeableConceptHGNC gene symbol
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsGene
Binding: ???? (preferred)
... observation-geneticsDNARegionName I0..1stringDNA region name
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsDNARegionName
... observation-geneticsAlleleName I0..1CodeableConceptName of allele
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAlleleName
Binding: ???? (preferred)
... observation-geneticsAllelicState I0..1CodeableConceptThe level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAllelicState
... observation-geneticsAllelicFrequency I0..1decimalAllele frequency
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsAllelicFrequency
... observation-geneticsCopyNumberEvent I0..1CodeableConceptCopy number variation
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsCopyNumberEvent
... observation-geneticsGenomicSourceClass I0..1CodeableConceptGenomic source class
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsGenomicSourceClass
... observation-geneticsPhaseSet I0..1uriPhase set identifier (UUID/OID)
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsPhaseSet
... observation-geneticsSequence I0..*Reference(Sequence)Sequence
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsSequence
... observation-geneticsInterpretation I0..1Reference(Observation)Clinical interpretations for variant
URL: http://hl7.org/fhir/StructureDefinition/observation-geneticsInterpretation
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn Σ0..*Reference(CarePlan), Reference(DeviceRequest), Reference(ImmunizationRecommendation), Reference(MedicationRequest), Reference(NutritionOrder), Reference(ProcedureRequest), Reference(ReferralRequest)Fulfills plan, proposal or order
... status ?!Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category 0..*CodeableConceptClassification of type of observation
Binding: Observation Category Codes (preferred)
... code Σ1..1CodeableConceptType of observation (code / type)
Binding: LOINC Codes (example)
... subject Σ0..1Reference(Patient), Reference(Group), Reference(Device), Reference(Location)Who and/or what this is about
... context 0..1Reference(Encounter), Reference(EpisodeOfCare)Healthcare event during which this observation is made
... effective[x] Σ0..1dateTime, PeriodClinically relevant time/time-period for observation
... issued Σ0..1instantDate/Time this was made available
... performer Σ0..*Reference(Practitioner), Reference(Organization), Reference(Patient), Reference(RelatedPerson)Who is responsible for the observation
... value[x] ΣI0..1Quantity, CodeableConcept, string, boolean, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual result
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: Observation Value Absent Reason (extensible)
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
... comment 0..1stringComments about result
... bodySite 0..1CodeableConceptObserved body part
Binding: SNOMED CT Body Structures (example)
... method 0..1CodeableConceptHow it was done
Binding: Observation Methods (example)
... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(Device), Reference(DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... type 0..1CodeableConceptReference range qualifier
Binding: Observation Reference Range Meaning Codes (extensible)
.... appliesTo 0..*CodeableConceptReference range population
Binding: Observation Reference Range Applies To Codes (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... related ΣI0..*BackboneElementResource related to this observation
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... type 0..1codehas-member | derived-from | sequel-to | replaces | qualified-by | interfered-by
Binding: ObservationRelationshipType (required)
.... target 1..1Reference(Observation), Reference(QuestionnaireResponse), Reference(Sequence)Resource that is related to this one
... component ΣI0..*BackboneElementComponent results
.... id 0..1stringxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored
.... code Σ1..1CodeableConceptType of component observation (code / type)
Binding: LOINC Codes (example)
.... value[x] Σ0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: Observation Value Absent Reason (extensible)
.... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
.... referenceRange 0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result

doco Documentation for this format

XML Template

<!-- Observation-genetics -->doco

<Observation xmlns="http://hl7.org/fhir"
>
  <!-- from Element: extension -->
 <id value="[id]"/><!-- 0..1 Logical id of this artifact -->
 <meta><!-- 0..1 Meta Metadata about the resource --></meta>
 <implicitRules value="[uri]"/><!-- 0..1 A set of rules under which this content was created -->
 <language value="[code]"/><!-- 0..1 Language of the resource content  -->
 <text><!-- 0..1 Narrative 
     Text summary of the resource, for human interpretation --></text>
 <contained><!-- 0..* Resource Contained, inline Resources --></contained>
 <modifierExtension><!-- 0..* Extension  Extensions that cannot be ignored  --></modifierExtension>
 <identifier><!-- 0..* Identifier 
     Business Identifier for observation --></identifier>
 <basedOn><!-- 0..* Reference(CarePlan)|Reference(DeviceRequest)|Reference(ImmunizationRecommendation)|Reference(MedicationRequest)|
   Reference(NutritionOrder)|Reference(ProcedureRequest)|Reference(ReferralRequest) Fulfills plan, proposal or order --></basedOn>
 <status value="[code]"/><!-- 1..1 registered | preliminary | final | amended +  -->
 <category><!-- 0..* CodeableConcept Classification of  type of observation  --></category>
 <code><!-- 1..1 CodeableConcept Type of observation (code / type)  --></code>
 <subject><!-- 0..1 Reference(Patient)|Reference(Group)|Reference(Device)|Reference(Location) 
     Who and/or what this is about --></subject>
 <context><!-- 0..1 Reference(Encounter)|Reference(EpisodeOfCare) 
     Healthcare event during which this observation is made --></context>
 <effective[x]><!-- 0..1 dateTime|Period 
     Clinically relevant time/time-period for observation --></effective[x]>
 <issued value="[instant]"/><!-- 0..1 Date/Time this was made available -->
 <performer><!-- 0..* Reference(Practitioner)|Reference(Organization)|Reference(Patient)|Reference(RelatedPerson) 
     Who is responsible for the observation --></performer>
 <value[x]><!-- 0..1 Quantity|CodeableConcept|string|boolean|Range|
   Ratio|SampledData|Attachment|time|dateTime|Period Actual result --></value[x]>
 <dataAbsentReason><!-- 0..1 CodeableConcept Why the result is missing  --></dataAbsentReason>
 <interpretation><!-- 0..1 CodeableConcept High, low, normal, etc.  --></interpretation>
 <comment value="[string]"/><!-- 0..1 Comments about result -->
 <bodySite><!-- 0..1 CodeableConcept Observed body part  --></bodySite>
 <method><!-- 0..1 CodeableConcept How it was done  --></method>
 <specimen><!-- 0..1 Reference(Specimen) Specimen used for this observation --></specimen>
 <device><!-- 0..1 Reference(Device)|Reference(DeviceMetric) (Measurement) Device --></device>
 <referenceRange> ?? 0..* BackboneElement  <!-- ?? 0..* Provides guide for interpretation -->
  <modifierExtension><!-- 0..* Extension  Extensions that cannot be ignored  --></modifierExtension>
  <low><!-- 0..1 Quantity 
      Low Range, if relevant --></low>
  <high><!-- 0..1 Quantity 
      High Range, if relevant --></high>
  <type><!-- 0..1 CodeableConcept Reference range qualifier  --></type>
  <appliesTo><!-- 0..* CodeableConcept Reference range population  --></appliesTo>
  <age><!-- 0..1 Range 
      Applicable age range, if relevant --></age>
  <text value="[string]"/><!-- 0..1 Text based reference range in an observation -->
 </referenceRange>
 <related> ?? 0..* BackboneElement  <!-- ?? 0..* Resource related to this observation -->
  <modifierExtension><!-- 0..* Extension  Extensions that cannot be ignored  --></modifierExtension>
  <type value="[code]"/><!-- 0..1 has-member | derived-from | sequel-to | replaces | qualified-by | interfered-by  -->
  <target><!-- 1..1 Reference(Observation)|Reference(QuestionnaireResponse)|Reference(Sequence) 
      Resource that is related to this one --></target>
 </related>
 <component> ?? 0..* BackboneElement  <!-- ?? 0..* Component results -->
  <modifierExtension><!-- 0..* Extension  Extensions that cannot be ignored  --></modifierExtension>
  <code><!-- 1..1 CodeableConcept Type of component observation (code / type)  --></code>
  <value[x]><!-- 0..1 Quantity|CodeableConcept|string|
    Range|Ratio|SampledData|Attachment|time|dateTime|Period 
      Actual component result --></value[x]>
  <dataAbsentReason><!-- 0..1 CodeableConcept Why the component result is missing  --></dataAbsentReason>
  <interpretation><!-- 0..1 CodeableConcept High, low, normal, etc.  --></interpretation>
  <referenceRange><!-- See #Observation.referenceRange  Provides guide for interpretation of component result --></referenceRange>
 </component>
</Observation>

JSON Template

{ // Observation-genetics
  // from Element: extension
    "meta" : { Meta }, //Metadata about the resource
    "implicitRules" : "<uri>", //A set of rules under which this content was created
    "language" : "<code>", //Language of the resource content 
    "text" : { Narrative }, //Text summary of the resource, for human interpretation
    "contained" : [{ Resource }], //Contained, inline Resources
    "extension" : [ //  sliced by value:url  in the specified orderOpen
      { // DNA sequence variant // C?
        // from Element: extension
      },
      { // DNA sequence variant ID // C?
        // from Element: extension
      },
      { // DNA sequence variant type // C?
        // from Element: extension
      },
      { // Amino acid change // C?
        // from Element: extension
      },
      { // Amino Acid Change Type // C?
        // from Element: extension
      },
      { // HGNC gene symbol // C?
        // from Element: extension
      },
      { // DNA region name // C?
        // from Element: extension
      },
      { // Name of allele // C?
        // from Element: extension
      },
      { // The level of occurrence of a single DNA sequence variant within a set of chromosomes: Heteroplasmic / Homoplasmic / Homozygous / Heterozygous / Hemizygous // C?
        // from Element: extension
      },
      { // Allele frequency // C?
        // from Element: extension
      },
      { // Copy number variation // C?
        // from Element: extension
      },
      { // Genomic source class // C?
        // from Element: extension
      },
      { // Phase set identifier (UUID/OID) // C?
        // from Element: extension
      },
      { // Sequence // C?
        // from Element: extension
      },
      { // Clinical interpretations for variant // C?
        // from Element: extension
      }
    ],
    "modifierExtension" : [{ Extension }], //Extensions that cannot be ignored
    "identifier" : [{ Identifier }], //Business Identifier for observation
// value[x]: Fulfills plan, proposal or order. One of these 7:
    "basedOn" : [{ Reference(CarePlan) }], //Fulfills plan, proposal or order
    "basedOn" : [{ Reference(DeviceRequest) }], //Fulfills plan, proposal or order
    "basedOn" : [{ Reference(ImmunizationRecommendation) }], //Fulfills plan, proposal or order
    "basedOn" : [{ Reference(MedicationRequest) }], //Fulfills plan, proposal or order
    "basedOn" : [{ Reference(NutritionOrder) }], //Fulfills plan, proposal or order
    "basedOn" : [{ Reference(ProcedureRequest) }], //Fulfills plan, proposal or order
    "basedOn" : [{ Reference(ReferralRequest) }], //Fulfills plan, proposal or order
    "status" : "<code>", // R! registered | preliminary | final | amended + 
    "category" : [{ CodeableConcept }], //Classification of  type of observation 
    "code" : { CodeableConcept }, // R! Type of observation (code / type) 
// value[x]: Who and/or what this is about. One of these 4:
    "subject" : { Reference(Patient) }, //Who and/or what this is about
    "subject" : { Reference(Group) }, //Who and/or what this is about
    "subject" : { Reference(Device) }, //Who and/or what this is about
    "subject" : { Reference(Location) }, //Who and/or what this is about
// value[x]: Healthcare event during which this observation is made. One of these 2:
    "context" : { Reference(Encounter) }, //Healthcare event during which this observation is made
    "context" : { Reference(EpisodeOfCare) }, //Healthcare event during which this observation is made
// value[x]: Clinically relevant time/time-period for observation. One of these 2:
    "effectiveDateTime" : "<dateTime>", //Clinically relevant time/time-period for observation
    "effectivePeriod" : { Period }, //Clinically relevant time/time-period for observation
    "issued" : "<instant>", //Date/Time this was made available
// value[x]: Who is responsible for the observation. One of these 4:
    "performer" : [{ Reference(Practitioner) }], //Who is responsible for the observation
    "performer" : [{ Reference(Organization) }], //Who is responsible for the observation
    "performer" : [{ Reference(Patient) }], //Who is responsible for the observation
    "performer" : [{ Reference(RelatedPerson) }], //Who is responsible for the observation
// value[x]: Actual result. One of these 11:
    "valueQuantity" : { Quantity }, //Actual result
    "valueCodeableConcept" : { CodeableConcept }, //Actual result
    "valueString" : "<string>", //Actual result
    "valueBoolean" : <boolean>, //Actual result
    "valueRange" : { Range }, //Actual result
    "valueRatio" : { Ratio }, //Actual result
    "valueSampledData" : { SampledData }, //Actual result
    "valueAttachment" : { Attachment }, //Actual result
    "valueTime" : "<time>", //Actual result
    "valueDateTime" : "<dateTime>", //Actual result
    "valuePeriod" : { Period }, //Actual result
    "dataAbsentReason" : { CodeableConcept } //Why the result is missing 
    "interpretation" : { CodeableConcept }, //High, low, normal, etc. 
    "comment" : "<string>", //Comments about result
    "bodySite" : { CodeableConcept }, //Observed body part 
    "method" : { CodeableConcept }, //How it was done 
    "specimen" : { Reference(Specimen) }, //Specimen used for this observation
// value[x]: (Measurement) Device. One of these 2:
    "device" : { Reference(Device) }, //(Measurement) Device
    "device" : { Reference(DeviceMetric) }, //(Measurement) Device
    "referenceRange" : [{ BackboneElement }], // C?Provides guide for interpretation
    "related" : [{ BackboneElement }], // C?Resource related to this observation
    "component" : [{ BackboneElement }], // C?Component results
  }

 

Other representations of profile: Schematron

10.1.14.6.2 Terminology Bindings

PathNameConformanceValueSet
Observation.languageCommon LanguagesextensibleCommon Languages
Observation.statusObservationStatusrequiredObservationStatus
Observation.categoryObservation Category CodespreferredObservation Category Codes
Observation.codeLOINC CodesexampleLOINC Codes
Observation.dataAbsentReasonObservation Value Absent ReasonextensibleObservation Value Absent Reason
Observation.interpretationObservation Interpretation CodesextensibleObservation Interpretation Codes
Observation.bodySiteSNOMED CT Body StructuresexampleSNOMED CT Body Structures
Observation.methodObservation MethodsexampleObservation Methods
Observation.referenceRange.typeObservation Reference Range Meaning CodesextensibleObservation Reference Range Meaning Codes
Observation.referenceRange.appliesToObservation Reference Range Applies To CodesexampleObservation Reference Range Applies To Codes
Observation.related.typeObservationRelationshipTyperequiredObservationRelationshipType
Observation.component.codeLOINC CodesexampleLOINC Codes
Observation.component.dataAbsentReasonObservation Value Absent ReasonextensibleObservation Value Absent Reason
Observation.component.interpretationObservation Interpretation CodesextensibleObservation Interpretation Codes

10.1.14.6.3 Constraints

IdPathDetailsRequirements
obs-3Observation.referenceRangeMust have at least a low or a high or text
Expression : low.exists() or high.exists() or text.exists()
.