HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE), v0.9.1

HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE), v0.9.1 FHIR Profiles - Local Development build (v0.9.1). See the Directory of published versions

GeneticVariantTested

 

The official URL for this profile is:

http://mcodeinitiative.org/us/mcode/StructureDefinition/onco-core-GeneticVariantTested

A test for a specific mutation on a particular gene. This profile is used to record whether a single discrete variant tested is present or absent (denoted as positive or negative respectively).

This profile builds on http://fhir.org/guides/argonaut/StructureDefinition/argo-observationresults.

This profile was published on Wed Oct 23 00:00:00 EDT 2019 as a draft by The MITRE Corporation.

Summary

Mandatory: 0 element (5 nested mandatory elements)
Must-Support: 4 elements
Fixed Value: 3 elements
Prohibited: 5 elements

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

Slices

This structure defines the following Slices:

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

Mapping Source

This structure represents the following mapping definition:

onco.core.GeneticVariantTested maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-observationresults:
  Language maps to language
  ImplicitRules maps to implicitRules
  Metadata.VersionId maps to meta.versionId
  Metadata.SourceSystem maps to meta.extension
  Metadata.Profile maps to meta.profile
  Metadata.LastUpdated maps to meta.lastUpdated
  Metadata.SecurityLabel maps to meta.security
  Metadata.Tag maps to meta.tag
  Narrative maps to text
  Identifier maps to identifier (slice on = type.coding.code; slice strategy = includes)
  ObservationBasedOn maps to extension
  ObservationPartOf maps to extension
  Status maps to status
  Category maps to category
  Code maps to code
  ObservationSubjectOfRecord maps to subject
  FocalSubject maps to modifierExtension
  CareContext maps to encounter
  RelevantTime maps to effective[x]
  StatementDateTime maps to issued
  LaboratoryObservationPerformer maps to performer (slice on = target.reference.resolve(); slice on type = profile; slice strategy = includes)
  DataValue maps to value[x]
  DataAbsentReason maps to dataAbsentReason
  Interpretation maps to interpretation
  Annotation maps to extension
  BodyLocation.Code maps to bodySite
  BodyLocation.Laterality maps to bodySite.extension
  BodyLocation.AnatomicalOrientation maps to bodySite.extension
  BodyLocation.RelationToLandmark maps to bodySite.extension
  Method maps to method
  Specimen maps to specimen
  Device maps to device
  ReferenceRange maps to referenceRange
  ReferenceRange.LowerBound maps to referenceRange.low
  ReferenceRange.UpperBound maps to referenceRange.high
  ReferenceRange.Type maps to referenceRange.meaning
  ReferenceRange.ApplicableSubpopulation maps to referenceRange.extension
  ReferenceRange.ApplicableAgeRange maps to referenceRange.age
  ReferenceRange.Text maps to referenceRange.text
  fix related.type to #has-member
  PanelMembers maps to related
  PanelMembers.Observation maps to related.target (slice at = related; slice on = target.reference.resolve(); slice on type = profile; slice strategy = includes)
  ObservationDerivedFrom maps to extension
  Components.ObservationComponent maps to component (slice on = code.coding.code; slice strategy = includes)
  Components.ObservationComponent.Code maps to component.code
  Components.ObservationComponent.DataValue maps to component.value[x]
  Components.ObservationComponent.DataAbsentReason maps to component.dataAbsentReason
  Components.ObservationComponent.ReferenceRange maps to component.referenceRange
  Components.ObservationComponent.ReferenceRange.LowerBound maps to component.referenceRange.low
  Components.ObservationComponent.ReferenceRange.UpperBound maps to component.referenceRange.high
  Components.ObservationComponent.ReferenceRange.Type maps to component.referenceRange.meaning
  Components.ObservationComponent.ReferenceRange.ApplicableAgeRange maps to component.referenceRange.age
  Components.ObservationComponent.ReferenceRange.Text maps to component.referenceRange.text

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation onco-core-GeneticVariantTested
... meta
.... extension Slice: Unordered, Open by value:url
.... obf-SourceSystem-extension 0..1uriSourceSystem
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SourceSystem-extension
... extension 1..*Slice: Unordered, Open by value:url
... obf-ObservationBasedOn-extension 0..*Reference(obf-ProcedureRequest | ReferralRequest)ObservationBasedOn
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ObservationBasedOn-extension
... obf-ObservationPartOf-extension 0..*Reference(obf-MedicationAdministration | obf-MedicationDispense | obf-MedicationStatement | obf-Procedure)ObservationPartOf
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ObservationPartOf-extension
... obf-Annotation-extension 0..*AnnotationAnnotation
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-Annotation-extension
... obf-ObservationDerivedFrom-extension 0..*Reference(DocumentReference | Media | obf-QuestionnaireResponse | obf-Observation)ObservationDerivedFrom
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ObservationDerivedFrom-extension
... onco-core-GeneStudied-extension S0..1CodeableConceptGeneStudied
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/onco-core-GeneStudied-extension
Binding: genenames (extensible)
... onco-core-VariantTested-extension S1..1(Complex)VariantTested
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/onco-core-VariantTested-extension
... modifierExtension (Slice Definition)Slice: Unordered, Open by value:url
... modifierExtension:focalsubject ?!S0..*FocalSubject
.... valueReference Reference(obf-Resource)Resource: Parent class for any item in clinical or administrative health-related system
... identifier (Slice Definition)Slice: Unordered, Open by value:type.coding.code
.... identifier:obf-AccessionIdentifier 0..1AccessionIdentifierAccessionIdentifier: Identifier assigned by the lab
.... identifier:obf-FillerOrderNumber 0..1FillerOrderNumberFillerOrderNumber: Identifier assigned by the lab carrying out the test
.... identifier:obf-PlacerOrderNumber 0..1PlacerOrderNumberPlacerOrderNumber: Identifier assigned by the requester of the lab
... category Binding: Observation Category Codes (extensible)
... code
.... coding 1..*(Slice Definition)Slice: Unordered, Open by value:code
..... coding:Fixed_41103-3 Σ1..1CodingGene XXX mutations found in Blood or Tissue by Molecular genetics method
...... system Fixed Value: http://loinc.org
...... code Fixed Value: 41103-3
... subject Reference(obf-Patient)The subject of an observation
... performer Reference(Practitioner | Organization)The practitioner that carried out the observation or action
... value[x] 1..1Binding: PositiveNegativeVS (required)
.... valueQuantityQuantity
.... valueCodeableConceptCodeableConcept
.... valueStringstring
.... valueRangeRange
.... valueRatioRatio
.... valueSampledDataSampledData
.... valueTimetime
.... valueDateTimedateTime
.... valuePeriodPeriod
... dataAbsentReason 0..0
... bodySite 0..0
... method SBinding: GeneticTestMethodVS (extensible)
... device Reference(http://fhir.org/guides/argonaut/StructureDefinition/argo-device)
... referenceRange 0..0
... related 0..0
... component 0..0

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*onco-core-GeneticVariantTested
obs-6: SHALL only be present if Observation.value[x] is not present
obs-7: Component code SHALL not be same as observation code
arg-2: If there is no component or related element then either a value[x] or a data absent reason must be present
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
.... obf-SourceSystem-extension 0..1uriSourceSystem
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SourceSystem-extension
.... versionId Σ0..1idVersion specific identifier
.... lastUpdated Σ0..1instantWhen the resource version last changed
.... profile Σ0..*uriProfiles this resource claims to conform to
.... security Σ0..*CodingSecurity Labels applied to this resource
Binding: All Security Labels (extensible)
.... tag Σ0..*CodingTags applied to this resource
Binding: (unbound) (example)
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: http://tools.ietf.org/html/bcp47 (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 1..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
... obf-ObservationBasedOn-extension 0..*Reference(obf-ProcedureRequest | ReferralRequest)ObservationBasedOn
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ObservationBasedOn-extension
... obf-ObservationPartOf-extension 0..*Reference(obf-MedicationAdministration | obf-MedicationDispense | obf-MedicationStatement | obf-Procedure)ObservationPartOf
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ObservationPartOf-extension
... obf-Annotation-extension 0..*AnnotationAnnotation
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-Annotation-extension
... obf-ObservationDerivedFrom-extension 0..*Reference(DocumentReference | Media | obf-QuestionnaireResponse | obf-Observation)ObservationDerivedFrom
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ObservationDerivedFrom-extension
... onco-core-GeneStudied-extension S0..1CodeableConceptGeneStudied
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/onco-core-GeneStudied-extension
Binding: genenames (extensible)
... onco-core-VariantTested-extension S1..1(Complex)VariantTested
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/onco-core-VariantTested-extension
... modifierExtension ?!0..*(Slice Definition)Extensions that cannot be ignored
Slice: Unordered, Open by exists:url
.... modifierExtension:focalsubject ?!S0..*FocalSubject
..... id 0..1idxml:id (or equivalent in JSON)
..... url 1..1uri"http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-FocalSubject-extension"
..... valueReference 1..1Reference(obf-Resource)Resource: Parent class for any item in clinical or administrative health-related system
... identifier 0..*(Slice Definition)Unique Id for this particular observation
Slice: Unordered, Open by value:type.coding.code
.... identifier:obf-AccessionIdentifier 0..1AccessionIdentifierAccessionIdentifier: Identifier assigned by the lab
.... identifier:obf-FillerOrderNumber 0..1FillerOrderNumberFillerOrderNumber: Identifier assigned by the lab carrying out the test
.... identifier:obf-PlacerOrderNumber 0..1PlacerOrderNumberPlacerOrderNumber: Identifier assigned by the requester of the lab
... status ?!S1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category S1..1CodeableConceptClassification of type of observation
Binding: Observation Category Codes (extensible)
Required Pattern: At least the following
.... id0..1stringxml:id (or equivalent in JSON)
.... extension0..*ExtensionAdditional Content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringxml:id (or equivalent in JSON)
..... extension0..*ExtensionAdditional Content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/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
..... userSelected1..1booleanIf this coding was chosen directly by the user
Fixed Value: false
.... text0..1stringPlain text representation of the concept
... code S1..1CodeableConceptLab Test Name
Binding: LOINC Codes (extensible)
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... coding Σ1..*(Slice Definition)Code defined by a terminology system
Slice: Unordered, Open by value:code
..... coding:Fixed_41103-3 Σ1..1CodingGene XXX mutations found in Blood or Tissue by Molecular genetics method
...... id 0..1idxml:id (or equivalent in JSON)
...... extension 0..*ExtensionAdditional Content defined by implementations
...... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... version Σ0..1stringVersion of the system - if relevant
...... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: 41103-3
...... display Σ0..1stringRepresentation defined by the system
...... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text Σ0..1stringPlain text representation of the concept
... subject S1..1Reference(obf-Patient)The subject of an observation
... encounter 0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] SI0..1Clinically relevant time/time-period for observation
arg-1: Datetime must be at least to day.
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
... issued Σ0..1instantDate/Time this was made available
... performer Σ0..*Reference(Practitioner | Organization)The practitioner that carried out the observation or action
... value[x] SI1..1Actual result
Binding: PositiveNegativeVS (required)
arg-3: SHALL use UCUM for coded quantity units.
arg-4: SHOULD use Snomed CT for coded Results
.... valueQuantityQuantity
.... valueCodeableConceptCodeableConcept
.... valueStringstring
.... valueRangeRange
.... valueRatioRatio
.... valueSampledDataSampledData
.... valueTimetime
.... valueDateTimedateTime
.... valuePeriodPeriod
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
... comments 0..1stringComments about result
... method S0..1CodeableConceptHow it was done
Binding: GeneticTestMethodVS (extensible)
... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(http://fhir.org/guides/argonaut/StructureDefinition/argo-device)(Measurement) Device

doco Documentation for this format

Summary

Mandatory: 0 element (5 nested mandatory elements)
Must-Support: 4 elements
Fixed Value: 3 elements
Prohibited: 5 elements

Structures

This structure refers to these other structures:

Extensions

This structure refers to these extensions:

Slices

This structure defines the following Slices:

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

Mapping Source

This structure represents the following mapping definition:

onco.core.GeneticVariantTested maps to http://fhir.org/guides/argonaut/StructureDefinition/argo-observationresults:
  Language maps to language
  ImplicitRules maps to implicitRules
  Metadata.VersionId maps to meta.versionId
  Metadata.SourceSystem maps to meta.extension
  Metadata.Profile maps to meta.profile
  Metadata.LastUpdated maps to meta.lastUpdated
  Metadata.SecurityLabel maps to meta.security
  Metadata.Tag maps to meta.tag
  Narrative maps to text
  Identifier maps to identifier (slice on = type.coding.code; slice strategy = includes)
  ObservationBasedOn maps to extension
  ObservationPartOf maps to extension
  Status maps to status
  Category maps to category
  Code maps to code
  ObservationSubjectOfRecord maps to subject
  FocalSubject maps to modifierExtension
  CareContext maps to encounter
  RelevantTime maps to effective[x]
  StatementDateTime maps to issued
  LaboratoryObservationPerformer maps to performer (slice on = target.reference.resolve(); slice on type = profile; slice strategy = includes)
  DataValue maps to value[x]
  DataAbsentReason maps to dataAbsentReason
  Interpretation maps to interpretation
  Annotation maps to extension
  BodyLocation.Code maps to bodySite
  BodyLocation.Laterality maps to bodySite.extension
  BodyLocation.AnatomicalOrientation maps to bodySite.extension
  BodyLocation.RelationToLandmark maps to bodySite.extension
  Method maps to method
  Specimen maps to specimen
  Device maps to device
  ReferenceRange maps to referenceRange
  ReferenceRange.LowerBound maps to referenceRange.low
  ReferenceRange.UpperBound maps to referenceRange.high
  ReferenceRange.Type maps to referenceRange.meaning
  ReferenceRange.ApplicableSubpopulation maps to referenceRange.extension
  ReferenceRange.ApplicableAgeRange maps to referenceRange.age
  ReferenceRange.Text maps to referenceRange.text
  fix related.type to #has-member
  PanelMembers maps to related
  PanelMembers.Observation maps to related.target (slice at = related; slice on = target.reference.resolve(); slice on type = profile; slice strategy = includes)
  ObservationDerivedFrom maps to extension
  Components.ObservationComponent maps to component (slice on = code.coding.code; slice strategy = includes)
  Components.ObservationComponent.Code maps to component.code
  Components.ObservationComponent.DataValue maps to component.value[x]
  Components.ObservationComponent.DataAbsentReason maps to component.dataAbsentReason
  Components.ObservationComponent.ReferenceRange maps to component.referenceRange
  Components.ObservationComponent.ReferenceRange.LowerBound maps to component.referenceRange.low
  Components.ObservationComponent.ReferenceRange.UpperBound maps to component.referenceRange.high
  Components.ObservationComponent.ReferenceRange.Type maps to component.referenceRange.meaning
  Components.ObservationComponent.ReferenceRange.ApplicableAgeRange maps to component.referenceRange.age
  Components.ObservationComponent.ReferenceRange.Text maps to component.referenceRange.text

Differential View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation onco-core-GeneticVariantTested
... meta
.... extension Slice: Unordered, Open by value:url
.... obf-SourceSystem-extension 0..1uriSourceSystem
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SourceSystem-extension
... extension 1..*Slice: Unordered, Open by value:url
... obf-ObservationBasedOn-extension 0..*Reference(obf-ProcedureRequest | ReferralRequest)ObservationBasedOn
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ObservationBasedOn-extension
... obf-ObservationPartOf-extension 0..*Reference(obf-MedicationAdministration | obf-MedicationDispense | obf-MedicationStatement | obf-Procedure)ObservationPartOf
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ObservationPartOf-extension
... obf-Annotation-extension 0..*AnnotationAnnotation
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-Annotation-extension
... obf-ObservationDerivedFrom-extension 0..*Reference(DocumentReference | Media | obf-QuestionnaireResponse | obf-Observation)ObservationDerivedFrom
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ObservationDerivedFrom-extension
... onco-core-GeneStudied-extension S0..1CodeableConceptGeneStudied
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/onco-core-GeneStudied-extension
Binding: genenames (extensible)
... onco-core-VariantTested-extension S1..1(Complex)VariantTested
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/onco-core-VariantTested-extension
... modifierExtension (Slice Definition)Slice: Unordered, Open by value:url
... modifierExtension:focalsubject ?!S0..*FocalSubject
.... valueReference Reference(obf-Resource)Resource: Parent class for any item in clinical or administrative health-related system
... identifier (Slice Definition)Slice: Unordered, Open by value:type.coding.code
.... identifier:obf-AccessionIdentifier 0..1AccessionIdentifierAccessionIdentifier: Identifier assigned by the lab
.... identifier:obf-FillerOrderNumber 0..1FillerOrderNumberFillerOrderNumber: Identifier assigned by the lab carrying out the test
.... identifier:obf-PlacerOrderNumber 0..1PlacerOrderNumberPlacerOrderNumber: Identifier assigned by the requester of the lab
... category Binding: Observation Category Codes (extensible)
... code
.... coding 1..*(Slice Definition)Slice: Unordered, Open by value:code
..... coding:Fixed_41103-3 Σ1..1CodingGene XXX mutations found in Blood or Tissue by Molecular genetics method
...... system Fixed Value: http://loinc.org
...... code Fixed Value: 41103-3
... subject Reference(obf-Patient)The subject of an observation
... performer Reference(Practitioner | Organization)The practitioner that carried out the observation or action
... value[x] 1..1Binding: PositiveNegativeVS (required)
.... valueQuantityQuantity
.... valueCodeableConceptCodeableConcept
.... valueStringstring
.... valueRangeRange
.... valueRatioRatio
.... valueSampledDataSampledData
.... valueTimetime
.... valueDateTimedateTime
.... valuePeriodPeriod
... dataAbsentReason 0..0
... bodySite 0..0
... method SBinding: GeneticTestMethodVS (extensible)
... device Reference(http://fhir.org/guides/argonaut/StructureDefinition/argo-device)
... referenceRange 0..0
... related 0..0
... component 0..0

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Observation I0..*onco-core-GeneticVariantTested
obs-6: SHALL only be present if Observation.value[x] is not present
obs-7: Component code SHALL not be same as observation code
arg-2: If there is no component or related element then either a value[x] or a data absent reason must be present
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
.... obf-SourceSystem-extension 0..1uriSourceSystem
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-SourceSystem-extension
.... versionId Σ0..1idVersion specific identifier
.... lastUpdated Σ0..1instantWhen the resource version last changed
.... profile Σ0..*uriProfiles this resource claims to conform to
.... security Σ0..*CodingSecurity Labels applied to this resource
Binding: All Security Labels (extensible)
.... tag Σ0..*CodingTags applied to this resource
Binding: (unbound) (example)
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: http://tools.ietf.org/html/bcp47 (required)
... text I0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 1..*ExtensionAdditional Content defined by implementations
Slice: Unordered, Open by value:url
... obf-ObservationBasedOn-extension 0..*Reference(obf-ProcedureRequest | ReferralRequest)ObservationBasedOn
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ObservationBasedOn-extension
... obf-ObservationPartOf-extension 0..*Reference(obf-MedicationAdministration | obf-MedicationDispense | obf-MedicationStatement | obf-Procedure)ObservationPartOf
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ObservationPartOf-extension
... obf-Annotation-extension 0..*AnnotationAnnotation
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-Annotation-extension
... obf-ObservationDerivedFrom-extension 0..*Reference(DocumentReference | Media | obf-QuestionnaireResponse | obf-Observation)ObservationDerivedFrom
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-ObservationDerivedFrom-extension
... onco-core-GeneStudied-extension S0..1CodeableConceptGeneStudied
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/onco-core-GeneStudied-extension
Binding: genenames (extensible)
... onco-core-VariantTested-extension S1..1(Complex)VariantTested
URL: http://mcodeinitiative.org/us/mcode/StructureDefinition/onco-core-VariantTested-extension
... modifierExtension ?!0..*(Slice Definition)Extensions that cannot be ignored
Slice: Unordered, Open by exists:url
.... modifierExtension:focalsubject ?!S0..*FocalSubject
..... id 0..1idxml:id (or equivalent in JSON)
..... url 1..1uri"http://mcodeinitiative.org/us/mcode/StructureDefinition/obf-FocalSubject-extension"
..... valueReference 1..1Reference(obf-Resource)Resource: Parent class for any item in clinical or administrative health-related system
... identifier 0..*(Slice Definition)Unique Id for this particular observation
Slice: Unordered, Open by value:type.coding.code
.... identifier:obf-AccessionIdentifier 0..1AccessionIdentifierAccessionIdentifier: Identifier assigned by the lab
.... identifier:obf-FillerOrderNumber 0..1FillerOrderNumberFillerOrderNumber: Identifier assigned by the lab carrying out the test
.... identifier:obf-PlacerOrderNumber 0..1PlacerOrderNumberPlacerOrderNumber: Identifier assigned by the requester of the lab
... status ?!S1..1coderegistered | preliminary | final | amended +
Binding: ObservationStatus (required)
... category S1..1CodeableConceptClassification of type of observation
Binding: Observation Category Codes (extensible)
Required Pattern: At least the following
.... id0..1stringxml:id (or equivalent in JSON)
.... extension0..*ExtensionAdditional Content defined by implementations
.... coding1..*CodingCode defined by a terminology system
Fixed Value: (complex)
..... id0..1stringxml:id (or equivalent in JSON)
..... extension0..*ExtensionAdditional Content defined by implementations
..... system1..1uriIdentity of the terminology system
Fixed Value: http://hl7.org/fhir/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
..... userSelected1..1booleanIf this coding was chosen directly by the user
Fixed Value: false
.... text0..1stringPlain text representation of the concept
... code S1..1CodeableConceptLab Test Name
Binding: LOINC Codes (extensible)
.... id 0..1idxml:id (or equivalent in JSON)
.... extension 0..*ExtensionAdditional Content defined by implementations
.... coding Σ1..*(Slice Definition)Code defined by a terminology system
Slice: Unordered, Open by value:code
..... coding:Fixed_41103-3 Σ1..1CodingGene XXX mutations found in Blood or Tissue by Molecular genetics method
...... id 0..1idxml:id (or equivalent in JSON)
...... extension 0..*ExtensionAdditional Content defined by implementations
...... system Σ0..1uriIdentity of the terminology system
Fixed Value: http://loinc.org
...... version Σ0..1stringVersion of the system - if relevant
...... code Σ0..1codeSymbol in syntax defined by the system
Fixed Value: 41103-3
...... display Σ0..1stringRepresentation defined by the system
...... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text Σ0..1stringPlain text representation of the concept
... subject S1..1Reference(obf-Patient)The subject of an observation
... encounter 0..1Reference(Encounter)Healthcare event during which this observation is made
... effective[x] SI0..1Clinically relevant time/time-period for observation
arg-1: Datetime must be at least to day.
.... effectiveDateTimedateTime
.... effectivePeriodPeriod
... issued Σ0..1instantDate/Time this was made available
... performer Σ0..*Reference(Practitioner | Organization)The practitioner that carried out the observation or action
... value[x] SI1..1Actual result
Binding: PositiveNegativeVS (required)
arg-3: SHALL use UCUM for coded quantity units.
arg-4: SHOULD use Snomed CT for coded Results
.... valueQuantityQuantity
.... valueCodeableConceptCodeableConcept
.... valueStringstring
.... valueRangeRange
.... valueRatioRatio
.... valueSampledDataSampledData
.... valueTimetime
.... valueDateTimedateTime
.... valuePeriodPeriod
... interpretation 0..1CodeableConceptHigh, low, normal, etc.
Binding: Observation Interpretation Codes (extensible)
... comments 0..1stringComments about result
... method S0..1CodeableConceptHow it was done
Binding: GeneticTestMethodVS (extensible)
... specimen 0..1Reference(Specimen)Specimen used for this observation
... device 0..1Reference(http://fhir.org/guides/argonaut/StructureDefinition/argo-device)(Measurement) Device

doco Documentation for this format

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

 

Terminology Bindings

PathConformanceValueSet / Code
Observation-argoprofile.meta.securityextensibleAll Security Labels
Observation-argoprofile.meta.tagexample
Observation-argoprofile.languagerequiredhttp://tools.ietf.org/html/bcp47
Observation-argoprofile.statusrequiredObservationStatus
Observation-argoprofile.categoryextensiblePattern: laboratory
Observation-argoprofile.codeextensibleLOINC Codes
Observation-argoprofile.valuexrequiredPositiveNegativeVS
Observation-argoprofile.interpretationextensibleObservation Interpretation Codes
Observation-argoprofile.methodextensibleGeneticTestMethodVS
Observation-argoprofile.referenceRange.meaningextensibleObservation Reference Range Meaning Codes
Observation-argoprofile.related.typerequiredFixed Value: has-member
Observation-argoprofile.component.codeexampleLOINC Codes
Observation-argoprofile.component.dataAbsentReasonextensibleObservation Value Absent Reason
Observation-argoprofile.component.referenceRange.meaningextensibleObservation Reference Range Meaning Codes

 

Constraints

IdPathDetailsRequirements
obs-6ObservationSHALL only be present if Observation.value[x] is not present
:
obs-7ObservationComponent code SHALL not be same as observation code
:
arg-2ObservationIf there is no component or related element then either a value[x] or a data absent reason must be present
: (component.empty() and related.empty()) implies (dataAbsentReason or value)
arg-1Observation.effective[x]Datetime must be at least to day.
: length() >= 8
arg-3Observation.value[x]SHALL use UCUM for coded quantity units.
: valueQuantity.system.empty() or valueQuantity.system = 'http://unitsofmeasure.org'
arg-4Observation.value[x]SHOULD use Snomed CT for coded Results
: valueCodeableConcept.coding.system.empty() or valueCodeableConcept.coding.system = 'http://snomed.info/sct'