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StructureDefinition: Genetics

The official URL for this profile is: 

http://hl7.org/fhir/StructureDefinition/observation-genetics-cg-prf-1a-genetics

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

This profile was published on Wed, Mar 18, 2015 00:00+1100 as a draft by Health Level Seven, Intl - Clinical Genomics.

Formal Views of Profile Content

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

This structure is derived from Observation.

unable to summarise extension (wrong count)

This structure is derived from Observation.

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 1..1Observation
... Extension 0..1ExtensionGeneticsSpecId
... extension 0..1ExtensionGenomeBuild
... extension 0..1ExtensionChr
... extension 0..1ExtensionGenomicRefSeqID
... extension 0..1ExtensionGenomic Start
... extension 0..1ExtensionGenomicEnd
... extension 0..1ExtensionRefAllele
... extension 0..1ExtensionObsAllele
... extension 0..1ExtensionHGNCgene
... extension 0..1ExtensionTransReferenceSeqID
... extension 0..1ExtensionHGVSdnaVariant
... extension 0..1ExtensionVariantId
... extension 0..1ExtensionRegionName
... extension 0..1ExtensionDNAvariantType
... extension 0..1ExtensionProteinReferenceSeq
... extension 0..1ExtensionHGVSproteinChange
... extension 0..1ExtensionProteinChangeType
... extension 0..1ExtensionAlleleName
... extension 0..1ExtensionGenomicSource
... extension 0..1ExtensionAllelicState
... extension 0..1ExtensionSpecies
... extension 0..1ExtensionCIGAR
... extension 0..1ExtensionAssessedCondition
... extension 0..1ExtensionGeneticsComment
... extension 0..1ExtensionGeneticsLab
... extension 0..1ExtensionGeneticsPtId
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I1..1ObservationMeasurements and simple assertions
obs-6: Shall only be present if Observation.value[x] is not present
... meta 0..1MetaMetadata about the resource
... implicitRules ?!0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: Language (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..1ExtensionGenomeBuild
... extension 0..1ExtensionChr
... extension 0..1ExtensionGenomicRefSeqID
... extension 0..1ExtensionGenomic Start
... extension 0..1ExtensionGenomicEnd
... extension 0..1ExtensionRefAllele
... extension 0..1ExtensionObsAllele
... extension 0..1ExtensionHGNCgene
... extension 0..1ExtensionTransReferenceSeqID
... extension 0..1ExtensionHGVSdnaVariant
... extension 0..1ExtensionVariantId
... extension 0..1ExtensionRegionName
... extension 0..1ExtensionDNAvariantType
... extension 0..1ExtensionProteinReferenceSeq
... extension 0..1ExtensionHGVSproteinChange
... extension 0..1ExtensionProteinChangeType
... extension 0..1ExtensionAlleleName
... extension 0..1ExtensionGenomicSource
... extension 0..1ExtensionAllelicState
... extension 0..1ExtensionSpecies
... extension 0..1ExtensionCIGAR
... extension 0..1ExtensionAssessedCondition
... extension 0..1ExtensionGeneticsComment
... extension 0..1ExtensionGeneticsLab
... extension 0..1ExtensionGeneticsPtId
... modifierExtension 0..*ExtensionExtensions that cannot be ignored
... code Σ1..1CodeableConceptType of observation (code / type)
Binding: ObservationType (example)
... value[x] Σ0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual result
Binding: ObservationValue (example)
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: ObservationValueAbsentReason (extensible)
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretation (extensible)
... comments 0..1stringComments about result
... applies[x] Σ0..1dateTime, PeriodPhysiologically Relevant time/time-period for observation
... issued Σ0..1instantDate/Time this was made available
... status ?! Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... reliability ?!0..1codeok | ongoing | early | questionable | calibrating | error +
Binding: ObservationReliability (required)
... bodySite[x] 0..1CodeableConcept, BodySiteObserved body part
Binding: BodySite (example)
... method 0..1CodeableConceptHow it was done
Binding: ObservationMethod (example)
... identifier 0..*IdentifierUnique Id for this particular observation
... subject Σ0..1Patient, Group, Device, LocationWho and/or what this is about
... specimen 0..1SpecimenSpecimen used for this observation
... performer Σ0..*Practitioner, Organization, Patient, RelatedPersonWho did the observation
... device 0..1Device, DeviceMetric(Measurement) Device
... encounter 0..1EncounterHealthcare event during which this observation is made
... referenceRange I0..*Provides guide for interpretation
obs-3: Must have at least a low or a high or text
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension 0..*ExtensionExtensions that cannot be ignored
.... low I0..1QuantityLow Range, if relevant
obs-4: Low range comparators can only be '>' or '>=' or empty
.... high I0..1QuantityHigh Range, if relevant
obs-5: High range comparators can only be '<' or '<=' or empty
.... meaning 0..1CodeableConceptIndicates the meaning/use of this range of this range
Binding: ObservationRangeMeaning (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... related Σ0..*Observations related to this observation
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension 0..*ExtensionExtensions that cannot be ignored
.... type 0..1codehas-component | has-member | derived-from | sequel-to | replaces | qualified-by | interfered-by
Binding: ObservationRelationshipType (required)
.... target 1..1ObservationObservation that is related to this one

todo

This structure is derived from Observation.

unable to summarise extension (wrong count)

Differential View

This structure is derived from Observation.

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 1..1Observation
... Extension 0..1ExtensionGeneticsSpecId
... extension 0..1ExtensionGenomeBuild
... extension 0..1ExtensionChr
... extension 0..1ExtensionGenomicRefSeqID
... extension 0..1ExtensionGenomic Start
... extension 0..1ExtensionGenomicEnd
... extension 0..1ExtensionRefAllele
... extension 0..1ExtensionObsAllele
... extension 0..1ExtensionHGNCgene
... extension 0..1ExtensionTransReferenceSeqID
... extension 0..1ExtensionHGVSdnaVariant
... extension 0..1ExtensionVariantId
... extension 0..1ExtensionRegionName
... extension 0..1ExtensionDNAvariantType
... extension 0..1ExtensionProteinReferenceSeq
... extension 0..1ExtensionHGVSproteinChange
... extension 0..1ExtensionProteinChangeType
... extension 0..1ExtensionAlleleName
... extension 0..1ExtensionGenomicSource
... extension 0..1ExtensionAllelicState
... extension 0..1ExtensionSpecies
... extension 0..1ExtensionCIGAR
... extension 0..1ExtensionAssessedCondition
... extension 0..1ExtensionGeneticsComment
... extension 0..1ExtensionGeneticsLab
... extension 0..1ExtensionGeneticsPtId

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I1..1ObservationMeasurements and simple assertions
obs-6: Shall only be present if Observation.value[x] is not present
... meta 0..1MetaMetadata about the resource
... implicitRules ?!0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: Language (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..1ExtensionGenomeBuild
... extension 0..1ExtensionChr
... extension 0..1ExtensionGenomicRefSeqID
... extension 0..1ExtensionGenomic Start
... extension 0..1ExtensionGenomicEnd
... extension 0..1ExtensionRefAllele
... extension 0..1ExtensionObsAllele
... extension 0..1ExtensionHGNCgene
... extension 0..1ExtensionTransReferenceSeqID
... extension 0..1ExtensionHGVSdnaVariant
... extension 0..1ExtensionVariantId
... extension 0..1ExtensionRegionName
... extension 0..1ExtensionDNAvariantType
... extension 0..1ExtensionProteinReferenceSeq
... extension 0..1ExtensionHGVSproteinChange
... extension 0..1ExtensionProteinChangeType
... extension 0..1ExtensionAlleleName
... extension 0..1ExtensionGenomicSource
... extension 0..1ExtensionAllelicState
... extension 0..1ExtensionSpecies
... extension 0..1ExtensionCIGAR
... extension 0..1ExtensionAssessedCondition
... extension 0..1ExtensionGeneticsComment
... extension 0..1ExtensionGeneticsLab
... extension 0..1ExtensionGeneticsPtId
... modifierExtension 0..*ExtensionExtensions that cannot be ignored
... code Σ1..1CodeableConceptType of observation (code / type)
Binding: ObservationType (example)
... value[x] Σ0..1Quantity, CodeableConcept, string, Range, Ratio, SampledData, Attachment, time, dateTime, PeriodActual result
Binding: ObservationValue (example)
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: ObservationValueAbsentReason (extensible)
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: ObservationInterpretation (extensible)
... comments 0..1stringComments about result
... applies[x] Σ0..1dateTime, PeriodPhysiologically Relevant time/time-period for observation
... issued Σ0..1instantDate/Time this was made available
... status ?! Σ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... reliability ?!0..1codeok | ongoing | early | questionable | calibrating | error +
Binding: ObservationReliability (required)
... bodySite[x] 0..1CodeableConcept, BodySiteObserved body part
Binding: BodySite (example)
... method 0..1CodeableConceptHow it was done
Binding: ObservationMethod (example)
... identifier 0..*IdentifierUnique Id for this particular observation
... subject Σ0..1Patient, Group, Device, LocationWho and/or what this is about
... specimen 0..1SpecimenSpecimen used for this observation
... performer Σ0..*Practitioner, Organization, Patient, RelatedPersonWho did the observation
... device 0..1Device, DeviceMetric(Measurement) Device
... encounter 0..1EncounterHealthcare event during which this observation is made
... referenceRange I0..*Provides guide for interpretation
obs-3: Must have at least a low or a high or text
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension 0..*ExtensionExtensions that cannot be ignored
.... low I0..1QuantityLow Range, if relevant
obs-4: Low range comparators can only be '>' or '>=' or empty
.... high I0..1QuantityHigh Range, if relevant
obs-5: High range comparators can only be '<' or '<=' or empty
.... meaning 0..1CodeableConceptIndicates the meaning/use of this range of this range
Binding: ObservationRangeMeaning (example)
.... age 0..1RangeApplicable age range, if relevant
.... text 0..1stringText based reference range in an observation
... related Σ0..*Observations related to this observation
.... extension 0..*ExtensionAdditional Content defined by implementations
.... modifierExtension 0..*ExtensionExtensions that cannot be ignored
.... type 0..1codehas-component | has-member | derived-from | sequel-to | replaces | qualified-by | interfered-by
Binding: ObservationRelationshipType (required)
.... target 1..1ObservationObservation that is related to this one

XML Template

JSON Template

todo

 

Other representations of profile: (todo)

Terminology Bindings

PathNameConformanceValueSet
Observation.languageLanguagerequiredhttp://tools.ietf.org/html/bcp47
Observation.codeObservationTypeexampleLOINC Codes
Observation.value[x]ObservationValueexampleSNOMED CT Codes
Observation.dataAbsentReasonObservationValueAbsentReasonextensibleObservation Value Absent Reason
Observation.interpretationObservationInterpretationextensibleObservation Interpretation Codes
Observation.statusObservationStatusrequiredObservationStatus
Observation.reliabilityObservationReliabilityrequiredObservationReliability
Observation.bodySite[x]BodySiteexampleSNOMED CT Body Structures
Observation.methodObservationMethodexampleObservation Methods
Observation.referenceRange.meaningObservationRangeMeaningexampleObservation Reference Range Meaning Codes
Observation.related.typeObservationRelationshipTyperequiredObservationRelationshipType

Constraints

IdPathNameDetails
obs-6Observationdata absent reasonShall only be present if Observation.value[x] is not present
XPath: not(exists(f:dataAbsentReason)) or (not(exists(*[starts-with(local-name(.), 'value')])))
obs-3Observation.referenceRangereference rangeMust have at least a low or a high or text
XPath: (exists(f:low) or exists(f:high)or exists(f:text))
obs-4Observation.referenceRange.lowlow range comparatorsLow range comparators can only be '>' or '>=' or empty
XPath: not(exists(f:comparator)) or boolean(f:comparator/@value = '<') or boolean(f:comparator/@value = '<=')
obs-5Observation.referenceRange.highhigh range comparatorsHigh range comparators can only be '<' or '<=' or empty
XPath: not(exists(f:comparator)) or boolean(f:comparator/@value = '>') or boolean(f:comparator/@value = '>=')
.