AU Core Implementation Guide
0.1.0-draft - Draft Australia flag

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Resource Profile: AU Core Specimen

Official URL: http://hl7.org.au/fhir/core/StructureDefinition/au-core-specimen Version: 0.1.0-draft
Standards status: Draft Maturity Level: 0 Computable Name: AUCoreSpecimen

Copyright/Legal: HL7 Australia© 2018+; Licensed Under Creative Commons No Rights Reserved.

This profile sets minimum expectations for a Specimen resource to record, search, and fetch specimens associated with a patient. It is based on the AU Base Specimen profile and identifies the additional mandatory core elements, extensions, vocabularies and value sets that SHALL be present in the Specimen when conforming to this profile. It provides the floor for standards development for specific uses cases in an Australian context.

Example usage scenarios

The following are example usage scenarios for this profile:

  • TBD
  • TBD

Profile specific implementation guidance

  • TBD

Usage:

  • Refer to this Resource Profile:
  • Examples for this Resource Profile: Specimen/nasoswab

Formal Views of Profile Content

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

This structure is derived from AUBaseSpecimen

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen C0..*AUBaseSpecimenA specimen in an Australian healthcare context
au-core-spc-04: The specimen shall at least have a valid identifier or method or type
... identifier SC0..*IdentifierExternal Identifier
... accessionIdentifier SC0..1IdentifierIdentifier assigned by the lab
... type SC0..1CodeableConceptKind of material that forms the specimen
... request S0..*Reference(AU Core ServiceRequest)Why the specimen was collected
... collection S1..1BackboneElementCollection details
.... collector S0..1Reference(AU Core Practitioner | AU Core PractitionerRole)Who collected the specimen
.... collected[x] S1..1dateTime, PeriodCollection time
.... method SC0..1CodeableConceptTechnique used to perform collection
.... bodySite SC0..1CodeableConceptAnatomical collection site
Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (extensible)
au-core-spc-03: If a coded body site is provided, at least one code shall be from SNOMED CT
.... fastingStatus[x] S0..1CodeableConcept, DurationWhether or how long patient abstained from food and/or drink

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSet
Specimen.collection.bodySiteextensiblehttps://healthterminologies.gov.au/fhir/ValueSet/body-site-1

Constraints

IdGradePath(s)DetailsRequirements
au-core-spc-03errorSpecimen.collection.bodySiteIf a coded body site is provided, at least one code shall be from SNOMED CT
: coding.exists() implies coding.where(system='http://snomed.info/sct').exists()
au-core-spc-04errorSpecimenThe specimen shall at least have a valid identifier or method or type
: type.exists() or collection.method.exists() or identifier.where(system.count() + value.count() >1).exists() or accessionIdentifier.where(system.count() + value.count() >1).exists()
NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen C0..*AUBaseSpecimenA specimen in an Australian healthcare context
au-core-spc-04: The specimen shall at least have a valid identifier or method or type
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier SΣC0..*IdentifierExternal Identifier
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.

... type SΣC0..1CodeableConceptKind of material that forms the specimen
Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 (preferred)
... subject SΣ1..1Reference(AU Core Patient)Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device
... request S0..*Reference(AU Core ServiceRequest)Why the specimen was collected
... collection S1..1BackboneElementCollection details
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... collector SΣ0..1Reference(AU Core Practitioner | AU Core PractitionerRole)Who collected the specimen
.... collected[x] SΣ1..1Collection time
..... collectedDateTimedateTime
..... collectedPeriodPeriod
.... method SC0..1CodeableConceptTechnique used to perform collection
Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 (preferred)
.... bodySite SC0..1CodeableConceptAnatomical collection site
Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (extensible)
au-core-spc-03: If a coded body site is provided, at least one code shall be from SNOMED CT
.... fastingStatus[x] SΣ0..1Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.

..... fastingStatusCodeableConceptCodeableConcept
..... fastingStatusDurationDuration

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet
Specimen.statusrequiredSpecimenStatus
Specimen.typepreferredhttps://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1
Specimen.collection.methodpreferredhttps://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1
Specimen.collection.bodySiteextensiblehttps://healthterminologies.gov.au/fhir/ValueSet/body-site-1
Specimen.collection.fastingStatus[x]extensibleHl7VSRelevantClincialInformation

Constraints

IdGradePath(s)DetailsRequirements
au-core-spc-03errorSpecimen.collection.bodySiteIf a coded body site is provided, at least one code shall be from SNOMED CT
: coding.exists() implies coding.where(system='http://snomed.info/sct').exists()
au-core-spc-04errorSpecimenThe specimen shall at least have a valid identifier or method or type
: type.exists() or collection.method.exists() or identifier.where(system.count() + value.count() >1).exists() or accessionIdentifier.where(system.count() + value.count() >1).exists()
NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen C0..*AUBaseSpecimenA specimen in an Australian healthcare context
au-core-spc-04: The specimen shall at least have a valid identifier or method or type
... 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
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier SΣC0..*IdentifierExternal Identifier
... accessionIdentifier SΣC0..1IdentifierIdentifier assigned by the lab
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.

... type SΣC0..1CodeableConceptKind of material that forms the specimen
Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 (preferred)
... subject SΣ1..1Reference(AU Core Patient)Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device
... receivedTime Σ0..1dateTimeThe time when specimen was received for processing
... parent 0..*Reference(AU Base Specimen)Specimen from which this specimen originated
... request S0..*Reference(AU Core ServiceRequest)Why the specimen was collected
... collection S1..1BackboneElementCollection details
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... collector SΣ0..1Reference(AU Core Practitioner | AU Core PractitionerRole)Who collected the specimen
.... collected[x] SΣ1..1Collection time
..... collectedDateTimedateTime
..... collectedPeriodPeriod
.... duration Σ0..1DurationHow long it took to collect specimen
.... quantity 0..1SimpleQuantityThe quantity of specimen collected
.... method SC0..1CodeableConceptTechnique used to perform collection
Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 (preferred)
.... bodySite SC0..1CodeableConceptAnatomical collection site
Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (extensible)
au-core-spc-03: If a coded body site is provided, at least one code shall be from SNOMED CT
.... fastingStatus[x] SΣ0..1Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.

..... fastingStatusCodeableConceptCodeableConcept
..... fastingStatusDurationDuration
... processing 0..*BackboneElementProcessing and processing step details
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... description 0..1stringTextual description of procedure
.... procedure 0..1CodeableConceptIndicates the treatment step applied to the specimen
Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen.

.... additive 0..*Reference(Substance)Material used in the processing step
.... time[x] 0..1Date and time of specimen processing
..... timeDateTimedateTime
..... timePeriodPeriod
... container 0..*BackboneElementDirect container of specimen (tube/slide, etc.)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... identifier Σ0..*IdentifierId for the container
.... description 0..1stringTextual description of the container
.... type 0..1CodeableConceptKind of container directly associated with specimen
Binding: SpecimenContainerType (example): Type of specimen container.

.... capacity 0..1SimpleQuantityContainer volume or size
.... specimenQuantity 0..1SimpleQuantityQuantity of specimen within container
.... additive[x] 0..1Additive associated with container
Binding: hl7VS-additivePreservative (example): Substance added to specimen container.

..... additiveCodeableConceptCodeableConcept
..... additiveReferenceReference(Substance)
... condition Σ0..*CodeableConceptState of the specimen
Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.


... note 0..*AnnotationComments

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet
Specimen.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
Specimen.statusrequiredSpecimenStatus
Specimen.typepreferredhttps://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1
Specimen.collection.methodpreferredhttps://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1
Specimen.collection.bodySiteextensiblehttps://healthterminologies.gov.au/fhir/ValueSet/body-site-1
Specimen.collection.fastingStatus[x]extensibleHl7VSRelevantClincialInformation
Specimen.processing.procedureexampleSpecimenProcessingProcedure
Specimen.container.typeexampleSpecimenContainerType
Specimen.container.additive[x]exampleHl7VSAdditivePreservative
Specimen.conditionextensibleHl7VSSpecimenCondition

Constraints

IdGradePath(s)DetailsRequirements
au-core-spc-03errorSpecimen.collection.bodySiteIf a coded body site is provided, at least one code shall be from SNOMED CT
: coding.exists() implies coding.where(system='http://snomed.info/sct').exists()

Differential View

This structure is derived from AUBaseSpecimen

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen C0..*AUBaseSpecimenA specimen in an Australian healthcare context
au-core-spc-04: The specimen shall at least have a valid identifier or method or type
... identifier SC0..*IdentifierExternal Identifier
... accessionIdentifier SC0..1IdentifierIdentifier assigned by the lab
... type SC0..1CodeableConceptKind of material that forms the specimen
... request S0..*Reference(AU Core ServiceRequest)Why the specimen was collected
... collection S1..1BackboneElementCollection details
.... collector S0..1Reference(AU Core Practitioner | AU Core PractitionerRole)Who collected the specimen
.... collected[x] S1..1dateTime, PeriodCollection time
.... method SC0..1CodeableConceptTechnique used to perform collection
.... bodySite SC0..1CodeableConceptAnatomical collection site
Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (extensible)
au-core-spc-03: If a coded body site is provided, at least one code shall be from SNOMED CT
.... fastingStatus[x] S0..1CodeableConcept, DurationWhether or how long patient abstained from food and/or drink

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSet
Specimen.collection.bodySiteextensiblehttps://healthterminologies.gov.au/fhir/ValueSet/body-site-1

Constraints

IdGradePath(s)DetailsRequirements
au-core-spc-03errorSpecimen.collection.bodySiteIf a coded body site is provided, at least one code shall be from SNOMED CT
: coding.exists() implies coding.where(system='http://snomed.info/sct').exists()
au-core-spc-04errorSpecimenThe specimen shall at least have a valid identifier or method or type
: type.exists() or collection.method.exists() or identifier.where(system.count() + value.count() >1).exists() or accessionIdentifier.where(system.count() + value.count() >1).exists()

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen C0..*AUBaseSpecimenA specimen in an Australian healthcare context
au-core-spc-04: The specimen shall at least have a valid identifier or method or type
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier SΣC0..*IdentifierExternal Identifier
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.

... type SΣC0..1CodeableConceptKind of material that forms the specimen
Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 (preferred)
... subject SΣ1..1Reference(AU Core Patient)Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device
... request S0..*Reference(AU Core ServiceRequest)Why the specimen was collected
... collection S1..1BackboneElementCollection details
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... collector SΣ0..1Reference(AU Core Practitioner | AU Core PractitionerRole)Who collected the specimen
.... collected[x] SΣ1..1Collection time
..... collectedDateTimedateTime
..... collectedPeriodPeriod
.... method SC0..1CodeableConceptTechnique used to perform collection
Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 (preferred)
.... bodySite SC0..1CodeableConceptAnatomical collection site
Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (extensible)
au-core-spc-03: If a coded body site is provided, at least one code shall be from SNOMED CT
.... fastingStatus[x] SΣ0..1Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.

..... fastingStatusCodeableConceptCodeableConcept
..... fastingStatusDurationDuration

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet
Specimen.statusrequiredSpecimenStatus
Specimen.typepreferredhttps://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1
Specimen.collection.methodpreferredhttps://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1
Specimen.collection.bodySiteextensiblehttps://healthterminologies.gov.au/fhir/ValueSet/body-site-1
Specimen.collection.fastingStatus[x]extensibleHl7VSRelevantClincialInformation

Constraints

IdGradePath(s)DetailsRequirements
au-core-spc-03errorSpecimen.collection.bodySiteIf a coded body site is provided, at least one code shall be from SNOMED CT
: coding.exists() implies coding.where(system='http://snomed.info/sct').exists()
au-core-spc-04errorSpecimenThe specimen shall at least have a valid identifier or method or type
: type.exists() or collection.method.exists() or identifier.where(system.count() + value.count() >1).exists() or accessionIdentifier.where(system.count() + value.count() >1).exists()

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen C0..*AUBaseSpecimenA specimen in an Australian healthcare context
au-core-spc-04: The specimen shall at least have a valid identifier or method or type
... 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
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier SΣC0..*IdentifierExternal Identifier
... accessionIdentifier SΣC0..1IdentifierIdentifier assigned by the lab
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.

... type SΣC0..1CodeableConceptKind of material that forms the specimen
Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 (preferred)
... subject SΣ1..1Reference(AU Core Patient)Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device
... receivedTime Σ0..1dateTimeThe time when specimen was received for processing
... parent 0..*Reference(AU Base Specimen)Specimen from which this specimen originated
... request S0..*Reference(AU Core ServiceRequest)Why the specimen was collected
... collection S1..1BackboneElementCollection details
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... collector SΣ0..1Reference(AU Core Practitioner | AU Core PractitionerRole)Who collected the specimen
.... collected[x] SΣ1..1Collection time
..... collectedDateTimedateTime
..... collectedPeriodPeriod
.... duration Σ0..1DurationHow long it took to collect specimen
.... quantity 0..1SimpleQuantityThe quantity of specimen collected
.... method SC0..1CodeableConceptTechnique used to perform collection
Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 (preferred)
.... bodySite SC0..1CodeableConceptAnatomical collection site
Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (extensible)
au-core-spc-03: If a coded body site is provided, at least one code shall be from SNOMED CT
.... fastingStatus[x] SΣ0..1Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.

..... fastingStatusCodeableConceptCodeableConcept
..... fastingStatusDurationDuration
... processing 0..*BackboneElementProcessing and processing step details
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... description 0..1stringTextual description of procedure
.... procedure 0..1CodeableConceptIndicates the treatment step applied to the specimen
Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen.

.... additive 0..*Reference(Substance)Material used in the processing step
.... time[x] 0..1Date and time of specimen processing
..... timeDateTimedateTime
..... timePeriodPeriod
... container 0..*BackboneElementDirect container of specimen (tube/slide, etc.)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... identifier Σ0..*IdentifierId for the container
.... description 0..1stringTextual description of the container
.... type 0..1CodeableConceptKind of container directly associated with specimen
Binding: SpecimenContainerType (example): Type of specimen container.

.... capacity 0..1SimpleQuantityContainer volume or size
.... specimenQuantity 0..1SimpleQuantityQuantity of specimen within container
.... additive[x] 0..1Additive associated with container
Binding: hl7VS-additivePreservative (example): Substance added to specimen container.

..... additiveCodeableConceptCodeableConcept
..... additiveReferenceReference(Substance)
... condition Σ0..*CodeableConceptState of the specimen
Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.


... note 0..*AnnotationComments

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet
Specimen.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
Specimen.statusrequiredSpecimenStatus
Specimen.typepreferredhttps://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1
Specimen.collection.methodpreferredhttps://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1
Specimen.collection.bodySiteextensiblehttps://healthterminologies.gov.au/fhir/ValueSet/body-site-1
Specimen.collection.fastingStatus[x]extensibleHl7VSRelevantClincialInformation
Specimen.processing.procedureexampleSpecimenProcessingProcedure
Specimen.container.typeexampleSpecimenContainerType
Specimen.container.additive[x]exampleHl7VSAdditivePreservative
Specimen.conditionextensibleHl7VSSpecimenCondition

Constraints

IdGradePath(s)DetailsRequirements
au-core-spc-03errorSpecimen.collection.bodySiteIf a coded body site is provided, at least one code shall be from SNOMED CT
: coding.exists() implies coding.where(system='http://snomed.info/sct').exists()

 

Other representations of profile: CSV, Excel, Schematron

Notes:

Below is an overview of the mandatory and optional search parameters. FHIR search operations and the syntax used to describe the interactions is described here.

Name Type Conformance Description Path
TBD TBD TBD TBD TBD

Mandatory Search Parameters

The following search parameters and search parameter combinations SHALL be supported:

Optional Search Parameters

The following search parameters and search parameter combinations SHOULD be supported: