Genomics Reporting Implementation Guide (STU1)

This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 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

StructureDefinition: InheritedDiseasePathogenicity

The official URL for this profile is: 

http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity

Formal Views of Profile Content

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

This structure is derived from Implication

Summary

Mandatory: 2 elements (4 nested mandatory elements)

Slices

This structure defines the following Slices:

  • The element Observation.component is sliced based on the value of pattern:code

This structure is derived from Implication

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*Inherited Disease Pathogenicity
... code 1..1CodeableConceptGenetic variation clinical significance
Required Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 53037-8
... valueCodeableConcept 1..1CodeableConceptPathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (extensible)
... component 0..*(Slice Definition)Slice: Unordered, Open by pattern:code
.... component:associated-phenotype 0..*BackboneElementAssociated phenotype
..... code 1..1CodeableConceptRequired Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81259-4
..... value[x] 1..1CodeableConceptBinding: (unbound) (example)
.... component:mode-of-inheritance 0..1BackboneElementMode of Inheritance
..... code 1..1CodeableConceptRequired Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 79742-3
..... value[x] 1..1CodeableConceptAutosomal dominant|Autosomal recessive|X-linked dominant|X-linked recessive|Y-linked|Codominant|Mitochondrial
Binding: LOINC Answer List LL3731-8 (preferred)

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Inherited Disease Pathogenicity
... id Σ0..1stringLogical id of this artifact
... meta ΣI0..1MetaMetadata about the resource
... implicitRules ?!ΣI0..1uriA set of rules under which this content was created
... language I0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension I0..*ExtensionExtension
Slice: Unordered, Open by value:url
... bodySite I0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... observation-secondaryFinding I0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible)
... RelatedArtifact I0..*RelatedArtifactCitations and supporting info
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RelatedArtifact
... modifierExtension ?!I0..*ExtensionExtensions that cannot be ignored
... identifier ΣI0..*IdentifierBusiness Identifier for observation
... basedOn ΣI0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf ΣI0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!ΣI1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category I1..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred)

Required Pattern: At least the following
.... id0..1stringUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... code ΣI1..1CodeableConceptGenetic variation clinical significance
Binding: LOINCCodes (example)
Required Pattern: At least the following
.... id0..1stringUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 53037-8
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject ΣI0..1Reference(Patient | Group | Location)Who and/or what the observation is about
... focus ΣI0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter ΣI0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] ΣI0..1(Slice Definition)Clinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime ΣI0..1dateTimeClinically relevant time/time-period for observation
... issued ΣI0..1instantDate/Time this version was made available
... performer ΣI0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ΣI0..1(Slice Definition)Actual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣI1..1CodeableConceptPathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (extensible)
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... note I0..*AnnotationDetails
... bodySite I0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example)
... method I0..1CodeableConceptHow it was done
Binding: ObservationMethods (example)
... specimen I0..1Reference(Specimen)Specimen used for this observation
... device I0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... type I0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred)
.... appliesTo I0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example)
.... age I0..1RangeApplicable age range, if relevant
.... text I0..1stringText based reference range in an observation
... hasMember ΣI0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom ΣI1..*(Slice Definition)Related measurements the observation is made from
Slice: Unordered, Open by pattern:resolve().code
.... derivedFrom:genotype ΣI0..*Reference(Genotype)Related measurements the observation is made from
.... derivedFrom:haplotype ΣI0..*Reference(Haplotype)Related measurements the observation is made from
.... derivedFrom:variant ΣI0..*Reference(Variant)Related measurements the observation is made from
... component ΣI0..*(Slice Definition)Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... value[x] ΣI0..1Actual component result
...... valueQuantityQuantity
...... valueCodeableConceptCodeableConcept
...... valueStringstring
...... valueBooleanboolean
...... valueIntegerinteger
...... valueRangeRange
...... valueRatioRatio
...... valueSampledDataSampledData
...... valueTimetime
...... valueDateTimedateTime
...... valuePeriodPeriod
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:evidence-level ΣI0..1BackboneElementLevel of Evidence
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93044-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] ΣI1..1CodeableConceptActual component result
Binding: LOINC Answer List LL5356-2 (preferred)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:associated-phenotype ΣI0..*BackboneElementAssociated phenotype
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81259-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] ΣI1..1CodeableConceptActual component result
Binding: (unbound) (example)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:mode-of-inheritance ΣI0..1BackboneElementMode of Inheritance
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 79742-3
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] ΣI1..1CodeableConceptAutosomal dominant|Autosomal recessive|X-linked dominant|X-linked recessive|Y-linked|Codominant|Mitochondrial
Binding: LOINC Answer List LL3731-8 (preferred)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result

doco Documentation for this format

This structure is derived from Implication

Summary

Mandatory: 2 elements (4 nested mandatory elements)

Slices

This structure defines the following Slices:

  • The element Observation.component is sliced based on the value of pattern:code

Differential View

This structure is derived from Implication

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation 0..*Inherited Disease Pathogenicity
... code 1..1CodeableConceptGenetic variation clinical significance
Required Pattern: At least the following
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 53037-8
... valueCodeableConcept 1..1CodeableConceptPathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (extensible)
... component 0..*(Slice Definition)Slice: Unordered, Open by pattern:code
.... component:associated-phenotype 0..*BackboneElementAssociated phenotype
..... code 1..1CodeableConceptRequired Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81259-4
..... value[x] 1..1CodeableConceptBinding: (unbound) (example)
.... component:mode-of-inheritance 0..1BackboneElementMode of Inheritance
..... code 1..1CodeableConceptRequired Pattern: At least the following
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 79742-3
..... value[x] 1..1CodeableConceptAutosomal dominant|Autosomal recessive|X-linked dominant|X-linked recessive|Y-linked|Codominant|Mitochondrial
Binding: LOINC Answer List LL3731-8 (preferred)

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*Inherited Disease Pathogenicity
... id Σ0..1stringLogical id of this artifact
... meta ΣI0..1MetaMetadata about the resource
... implicitRules ?!ΣI0..1uriA set of rules under which this content was created
... language I0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred)
Max Binding: AllLanguages
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension I0..*ExtensionExtension
Slice: Unordered, Open by value:url
... bodySite I0..1Reference(BodyStructure)Target anatomic location or structure
URL: http://hl7.org/fhir/StructureDefinition/bodySite
... observation-secondaryFinding I0..1CodeableConceptSecondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings
URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding
Binding: ObservationCategoryCodes (extensible)
... RelatedArtifact I0..*RelatedArtifactCitations and supporting info
URL: http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RelatedArtifact
... modifierExtension ?!I0..*ExtensionExtensions that cannot be ignored
... identifier ΣI0..*IdentifierBusiness Identifier for observation
... basedOn ΣI0..*Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)Fulfills plan, proposal or order
... partOf ΣI0..*Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)Part of referenced event
... status ?!ΣI1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category I1..*CodeableConceptClassification of type of observation
Binding: ObservationCategoryCodes (preferred)

Required Pattern: At least the following
.... id0..1stringUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: laboratory
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... code ΣI1..1CodeableConceptGenetic variation clinical significance
Binding: LOINCCodes (example)
Required Pattern: At least the following
.... id0..1stringUnique id for inter-element referencing
.... extension0..*ExtensionAdditional content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringUnique id for inter-element referencing
..... extension0..*ExtensionAdditional content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
..... version0..1stringVersion of the system - if relevant
..... code1..1codeSymbol in syntax defined by the system
Fixed Value: 53037-8
..... display0..1stringRepresentation defined by the system
..... userSelected0..1booleanIf this coding was chosen directly by the user
.... text0..1stringPlain text representation of the concept
... subject ΣI0..1Reference(Patient | Group | Location)Who and/or what the observation is about
... focus ΣI0..*Reference(Resource)What the observation is about, when it is not about the subject of record
... encounter ΣI0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] ΣI0..1(Slice Definition)Clinically relevant time/time-period for observation
Slice: Unordered, Closed by type:$this
.... effective[x]:effectiveDateTime ΣI0..1dateTimeClinically relevant time/time-period for observation
... issued ΣI0..1instantDate/Time this version was made available
... performer ΣI0..1Reference(Practitioner | Organization | Patient | RelatedPerson)Who is responsible for the observation
... value[x] ΣI0..1(Slice Definition)Actual result
Slice: Unordered, Closed by type:$this
.... value[x]:valueCodeableConcept ΣI1..1CodeableConceptPathogenic | Likely pathogenic | Uncertain significance | Likely benign | Benign
Binding: LOINC Answer List LL4034-6 (extensible)
... dataAbsentReason I0..1CodeableConceptWhy the result is missing
Binding: DataAbsentReason (extensible)
... note I0..*AnnotationDetails
... bodySite I0..1CodeableConceptObserved body part
Binding: SNOMEDCTBodyStructures (example)
... method I0..1CodeableConceptHow it was done
Binding: ObservationMethods (example)
... specimen I0..1Reference(Specimen)Specimen used for this observation
... device I0..1Reference(Device | DeviceMetric)(Measurement) Device
... referenceRange I0..*BackboneElementProvides guide for interpretation
obs-3: Must have at least a low or a high or text
.... id 0..1stringUnique id for inter-element referencing
.... extension I0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... low I0..1SimpleQuantityLow Range, if relevant
.... high I0..1SimpleQuantityHigh Range, if relevant
.... type I0..1CodeableConceptReference range qualifier
Binding: ObservationReferenceRangeMeaningCodes (preferred)
.... appliesTo I0..*CodeableConceptReference range population
Binding: ObservationReferenceRangeAppliesToCodes (example)
.... age I0..1RangeApplicable age range, if relevant
.... text I0..1stringText based reference range in an observation
... hasMember ΣI0..*Reference(Observation | QuestionnaireResponse | MolecularSequence)Related resource that belongs to the Observation group
... derivedFrom ΣI1..*(Slice Definition)Related measurements the observation is made from
Slice: Unordered, Open by pattern:resolve().code
.... derivedFrom:genotype ΣI0..*Reference(Genotype)Related measurements the observation is made from
.... derivedFrom:haplotype ΣI0..*Reference(Haplotype)Related measurements the observation is made from
.... derivedFrom:variant ΣI0..*Reference(Variant)Related measurements the observation is made from
... component ΣI0..*(Slice Definition)Component results
Slice: Unordered, Open by pattern:code
.... component:All Slices Content/Rules for all slices
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
..... value[x] ΣI0..1Actual component result
...... valueQuantityQuantity
...... valueCodeableConceptCodeableConcept
...... valueStringstring
...... valueBooleanboolean
...... valueIntegerinteger
...... valueRangeRange
...... valueRatioRatio
...... valueSampledDataSampledData
...... valueTimetime
...... valueDateTimedateTime
...... valuePeriodPeriod
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:evidence-level ΣI0..1BackboneElementLevel of Evidence
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 93044-6
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] ΣI1..1CodeableConceptActual component result
Binding: LOINC Answer List LL5356-2 (preferred)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:associated-phenotype ΣI0..*BackboneElementAssociated phenotype
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 81259-4
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] ΣI1..1CodeableConceptActual component result
Binding: (unbound) (example)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result
.... component:mode-of-inheritance ΣI0..1BackboneElementMode of Inheritance
..... id 0..1stringUnique id for inter-element referencing
..... extension I0..*ExtensionAdditional content defined by implementations
..... modifierExtension ?!ΣI0..*ExtensionExtensions that cannot be ignored even if unrecognized
..... code ΣI1..1CodeableConceptType of component observation (code / type)
Binding: LOINCCodes (example)
Required Pattern: At least the following
...... id0..1stringUnique id for inter-element referencing
...... extension0..*ExtensionAdditional content defined by implementations
...... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
....... id0..1stringUnique id for inter-element referencing
....... extension0..*ExtensionAdditional content defined by implementations
....... system1..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
....... version0..1stringVersion of the system - if relevant
....... code1..1codeSymbol in syntax defined by the system
Fixed Value: 79742-3
....... display0..1stringRepresentation defined by the system
....... userSelected0..1booleanIf this coding was chosen directly by the user
...... text0..1stringPlain text representation of the concept
..... value[x] ΣI1..1CodeableConceptAutosomal dominant|Autosomal recessive|X-linked dominant|X-linked recessive|Y-linked|Codominant|Mitochondrial
Binding: LOINC Answer List LL3731-8 (preferred)
..... dataAbsentReason I0..1CodeableConceptWhy the component result is missing
Binding: DataAbsentReason (extensible)
..... referenceRange I0..*Unknown reference to #Observation.referenceRange
Provides guide for interpretation of component result

doco Documentation for this format

 

Other representations of profile: Schematron

Terminology Bindings

PathConformanceValueSet / Code
Observation.languagepreferredCommonLanguages
Max Binding: AllLanguages
Observation.statusrequiredObservationStatus
Observation.categorypreferredPattern: laboratory
Observation.codeexamplePattern: LOINC code 53037-8
Observation.value[x]:valueCodeableConceptextensibleLOINC LL4034-6
Observation.dataAbsentReasonextensibleDataAbsentReason
Observation.bodySiteexampleSNOMEDCTBodyStructures
Observation.methodexampleObservationMethods
Observation.referenceRange.typepreferredObservationReferenceRangeMeaningCodes
Observation.referenceRange.appliesToexampleObservationReferenceRangeAppliesToCodes
Observation.component.codeexampleLOINCCodes
Observation.component.dataAbsentReasonextensibleDataAbsentReason
Observation.component:evidence-level.codeexamplePattern: LOINC code 93044-6
Observation.component:evidence-level.value[x]preferredLOINC LL5356-2
Observation.component:evidence-level.dataAbsentReasonextensibleDataAbsentReason
Observation.component:associated-phenotype.codeexamplePattern: LOINC code 81259-4
Observation.component:associated-phenotype.value[x]example
Observation.component:associated-phenotype.dataAbsentReasonextensibleDataAbsentReason
Observation.component:mode-of-inheritance.codeexamplePattern: LOINC code 79742-3
Observation.component:mode-of-inheritance.value[x]preferredLOINC LL3731-8
Observation.component:mode-of-inheritance.dataAbsentReasonextensibleDataAbsentReason

Constraints

IdPathDetailsRequirements
dom-2ObservationIf the resource is contained in another resource, it SHALL NOT contain nested Resources
: contained.contained.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-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-5ObservationIf a resource is contained in another resource, it SHALL NOT have a security label
: contained.meta.security.empty()
dom-6ObservationA resource should have narrative for robust management
: text.`div`.exists()
obs-6ObservationdataAbsentReason SHALL only be present if Observation.value[x] is not present
: dataAbsentReason.empty() or value.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.intersect(%resource.code.coding).exists()).empty()
ele-1Observation.metaAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.implicitRulesAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.languageAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.textAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.extensionAll FHIR elements must have a @value or children
: hasValue() or (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() or (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() or (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() or (children().count() > id.count())
ext-1Observation.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.identifierAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.basedOnAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.partOfAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.statusAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.categoryAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.subjectAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.focusAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.encounterAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.effective[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.effective[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.issuedAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.performerAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.noteAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.bodySiteAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.methodAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.specimenAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.deviceAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (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.referenceRange.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.referenceRange.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.referenceRange.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.referenceRange.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.referenceRange.lowAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.referenceRange.highAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.referenceRange.typeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.referenceRange.appliesToAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.referenceRange.ageAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.referenceRange.textAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.hasMemberAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.derivedFromAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.derivedFromAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.derivedFromAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.derivedFromAll 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.component.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.component.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.component.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.component.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.component.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.component.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.component.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.component.referenceRangeAll 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.component.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.component.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.component.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.component.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.component.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.component.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.component.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.component.referenceRangeAll 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.component.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.component.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.component.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.component.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.component.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.component.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.component.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.component.referenceRangeAll 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.component.extensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.component.extensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.component.modifierExtensionAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ext-1Observation.component.modifierExtensionMust have either extensions or value[x], not both
: extension.exists() != value.exists()
ele-1Observation.component.codeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.component.value[x]All FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.component.dataAbsentReasonAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())
ele-1Observation.component.referenceRangeAll FHIR elements must have a @value or children
: hasValue() or (children().count() > id.count())