This page is part of the Genetic Reporting Implementation Guide (v0.1.0: STU 1 Ballot 1) based on FHIR v3.3.0. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

2.7 StructureDefinition: Genetic analysis overall interpretation

The official URL for this profile is: 

http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/obs-overall

2.7.2 Formal Views of Profile Content

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

This structure is derived from Genetic Observation Common Properties

Summary

Mandatory: 2 elements
Must-Support: 3 elements

This structure is derived from Genetic Observation Common Properties

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*Genetic analysis overall interpretation
... code S1..1CodeableConceptDiscrete variation analysis overall interpretation
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"51968-6"}]}
... valueCodeableConcept S1..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodPositive | Negative | Inconclusive | Failure
Binding: LOINC Answer List LL541-4 (required)
... specimen S0..1Reference(Specimen)Specimen examined

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Genetic analysis overall interpretation
... 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
... body-structure SI0..1Reference(BodyStructure)Extension
URL: http://hl7.org/fhir/StructureDefinition/body-structure
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn SΣ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category S1..*CodeableConceptClassification of type of observation
Binding: Observation Category Codes (preferred)

Required Pattern: {"coding":[{"system":"http://hl7.org/fhir/observation-category","code":"laboratory"}]}
... code SΣ1..1CodeableConceptDiscrete variation analysis overall interpretation
Binding: LOINC Codes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"51968-6"}]}
... subject SΣ0..1Reference(Patient | Group | Location)Who and/or what this is about
... focus Σ0..1Reference(Resource)The "focal point" of the observation
... context 0..1Reference(Encounter | EpisodeOfCare)Healthcare event during which this observation is made
... effective[x] SΣ0..1dateTime, Period, TimingAssessment of overall results
... issued SΣ0..1instantAssessment of deletion/duplication results
... performer SΣ0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Genes, drugs and/or conditions tested with no findings
... value[x] SΣI1..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodPositive | Negative | Inconclusive | Failure
Binding: LOINC Answer List LL541-4 (required)
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (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 S0..1Reference(Specimen)Specimen examined
... device 0..1Reference(Device | DeviceComponent | 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
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | Sequence)Related resource that belongs to the Observation group
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | Sequence)Related measurements the observation is made from
... 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, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (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

This structure is derived from Genetic Observation Common Properties

Summary

Mandatory: 2 elements
Must-Support: 3 elements

Differential View

This structure is derived from Genetic Observation Common Properties

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*Genetic analysis overall interpretation
... code S1..1CodeableConceptDiscrete variation analysis overall interpretation
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"51968-6"}]}
... valueCodeableConcept S1..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodPositive | Negative | Inconclusive | Failure
Binding: LOINC Answer List LL541-4 (required)
... specimen S0..1Reference(Specimen)Specimen examined

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Genetic analysis overall interpretation
... 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
... body-structure SI0..1Reference(BodyStructure)Extension
URL: http://hl7.org/fhir/StructureDefinition/body-structure
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierBusiness Identifier for observation
... basedOn SΣ0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf Σ0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!SΣ1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category S1..*CodeableConceptClassification of type of observation
Binding: Observation Category Codes (preferred)

Required Pattern: {"coding":[{"system":"http://hl7.org/fhir/observation-category","code":"laboratory"}]}
... code SΣ1..1CodeableConceptDiscrete variation analysis overall interpretation
Binding: LOINC Codes (example)
Required Pattern: {"coding":[{"system":"http://loinc.org","code":"51968-6"}]}
... subject SΣ0..1Reference(Patient | Group | Location)Who and/or what this is about
... focus Σ0..1Reference(Resource)The "focal point" of the observation
... context 0..1Reference(Encounter | EpisodeOfCare)Healthcare event during which this observation is made
... effective[x] SΣ0..1dateTime, Period, TimingAssessment of overall results
... issued SΣ0..1instantAssessment of deletion/duplication results
... performer SΣ0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Genes, drugs and/or conditions tested with no findings
... value[x] SΣI1..1Quantity, CodeableConcept, string, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodPositive | Negative | Inconclusive | Failure
Binding: LOINC Answer List LL541-4 (required)
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (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 S0..1Reference(Specimen)Specimen examined
... device 0..1Reference(Device | DeviceComponent | 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
... hasMember Σ0..*Reference(Observation | QuestionnaireResponse | Sequence)Related resource that belongs to the Observation group
... derivedFrom Σ0..*Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | Sequence)Related measurements the observation is made from
... 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, boolean, integer, Range, Ratio, SampledData, time, dateTime, PeriodActual component result
.... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (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

 

Other representations of profile: Schematron

2.7.3 Terminology Bindings

Terminology Bindings

PathNameConformanceValueSet
Observation.languageCommon LanguagesextensibleCommon Languages
Observation.statusObservationStatusrequiredObservationStatus
Observation.categoryObservation Category CodespreferredObservation Category Codes
Observation.codeLOINC CodesexampleLOINC Codes
Observation.value[x]LOINC LL541-4requiredLOINC LL541-4
Observation.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
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.component.codeLOINC CodesexampleLOINC Codes
Observation.component.dataAbsentReasonDataAbsentReasonextensibleDataAbsentReason
Observation.component.interpretationObservation Interpretation CodesextensibleObservation Interpretation Codes

2.7.4 Constraints

Constraints

IdPathDetailsRequirements
dom-2ObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.empty()
dom-1ObservationIf the resource is contained in another resource, it SHALL NOT contain any narrative
: contained.text.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.all(('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists())
obs-7ObservationIf Observation.code is the same as a 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()
ele-1Observation.extensionAll FHIR elements must have a @value or children
: hasValue() | (children().count() > id.count())
ext-1Observation.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.extensionAll FHIR elements must have a @value or children
: hasValue() | (children().count() > id.count())
ext-1Observation.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.referenceRangeAll FHIR elements must have a @value or children
: hasValue() | (children().count() > id.count())
obs-3Observation.referenceRangeMust have at least a low or a high or text
: low.exists() or high.exists() or text.exists()
ele-1Observation.componentAll FHIR elements must have a @value or children
: hasValue() | (children().count() > id.count())