AU Core Implementation Guide
0.2.0-preview - QA Preview Australia flag

This page is part of the Australian Core IG (v0.2.0-preview: AU Core) based on FHIR R4. For a full list of available versions, see the Directory of published versions

Resource Profile: AU Core Specimen

Official URL: http://hl7.org.au/fhir/core/StructureDefinition/au-core-specimen Version: 0.2.0-preview
Standards status: Draft Maturity Level: 0 Computable Name: AUCoreSpecimen

Copyright/Legal: Used by permission of HL7 International, all rights reserved Creative Commons License. HL7 Australia© 2022+; 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.

Usage scenarios

The following are example usage scenarios for this profile:

  • Query specimens associated with a patient referenced by another resource
  • Record or update a specimen associated with a patient referenced by another resource
  • Read specimens associated with a patient referenced by another resource

Comparison with other national and international specifications

A resource conforming to this profile:

  • MAY be conformant to Specimen (IPS) if patient is supported as Specimen.subject.reference
  • MAY be conformant to US Core Specimen if Specimen.type is included

No equivalent International Patient Access profile.

Conformance in reverse is not guaranteed, i.e. a resource conforming to International Patient Summary or US Core MAY NOT conform to AU Core.

Profile specific implementation guidance

  • a collected specimen SHALL included the relevant collected time in Specimen.collection.collectedDateTime or Specimen.collection.collectedPeriod.

Usage:

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 0..*AUBaseSpecimenA specimen in an Australian healthcare context
... identifier S0..*IdentifierExternal Identifier
... accessionIdentifier S0..1IdentifierIdentifier assigned by the lab
... type S1..1CodeableConceptKind of material that forms the specimen
... request S0..*Reference(AU Core ServiceRequest)Why the specimen was collected
... collection S0..1BackboneElementCollection details
.... collector S0..1Reference(AU Core Practitioner | AU Core PractitionerRole)Who collected the specimen
.... collected[x] S1..1dateTime, PeriodCollection time
.... method S0..1CodeableConceptTechnique used to perform collection
.... bodySite SC0..1CodeableConceptAnatomical collection site
Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (extensible)
au-core-spc-01: 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-01errorSpecimen.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()
NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*AUBaseSpecimenA specimen in an Australian healthcare context
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier SΣ0..*IdentifierExternal Identifier
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.

... type SΣ1..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 S0..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 S0..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-01: 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-01errorSpecimen.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()
NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*AUBaseSpecimenA specimen in an Australian healthcare context
... 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 SΣ0..*IdentifierExternal Identifier
... accessionIdentifier SΣ0..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 SΣ1..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 S0..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 S0..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-01: 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-01errorSpecimen.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 0..*AUBaseSpecimenA specimen in an Australian healthcare context
... identifier S0..*IdentifierExternal Identifier
... accessionIdentifier S0..1IdentifierIdentifier assigned by the lab
... type S1..1CodeableConceptKind of material that forms the specimen
... request S0..*Reference(AU Core ServiceRequest)Why the specimen was collected
... collection S0..1BackboneElementCollection details
.... collector S0..1Reference(AU Core Practitioner | AU Core PractitionerRole)Who collected the specimen
.... collected[x] S1..1dateTime, PeriodCollection time
.... method S0..1CodeableConceptTechnique used to perform collection
.... bodySite SC0..1CodeableConceptAnatomical collection site
Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (extensible)
au-core-spc-01: 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-01errorSpecimen.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()

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*AUBaseSpecimenA specimen in an Australian healthcare context
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier SΣ0..*IdentifierExternal Identifier
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.

... type SΣ1..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 S0..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 S0..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-01: 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-01errorSpecimen.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()

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*AUBaseSpecimenA specimen in an Australian healthcare context
... 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 SΣ0..*IdentifierExternal Identifier
... accessionIdentifier SΣ0..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 SΣ1..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 S0..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 S0..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-01: 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-01errorSpecimen.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 and combined search parameters. FHIR search operations and the syntax used to describe the interactions is described here.

Any search parameter defined in FHIR may be ‘allowed’ by the system unless explicitly marked as “SHALL NOT”. A few items are marked as MAY in this implementation guide to highlight their potential relevance.

Parameter(s) Conformance Type(s) Requirements (when used alone or in combination)
patient SHALL reference The client SHALL provide at least an id value and MAY provide both the Type and id values. The server SHALL support both.
_id SHOULD token
patient.identifier SHOULD reference.token The client SHALL provide both the system and code values. The server SHALL support both.

The client SHOULD support search using IHI, Medicare Number, and DVA Number identifiers as defined in the AU Core Patient profile. The server SHOULD support search using the using IHI, Medicare Number, and DVA Number identifiers as defined in the AU Core Patient profile.

Mandatory Search Parameters:

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

  1. SHALL support searching using the patient search parameter:
    • SHALL support these _revinclude parameters: Provenance:target
    • SHOULD support chained searching of patient canonical identifier patient.identifier (e.g. patient.identifier=[system|][code]

    GET [base]/Specimen?patient={Type/}[id] or optionallyGET [base]/Specimen?patient.identifier=[system|][code]

    Example:

    1. GET [base]/Specimen?patient=5678
    2. GET [base]/Specimen?patient.identifier=http://ns.electronichealth.net.au/id/medicare-number|32788511952
    3. GET [base]/Specimen?patient.identifier=http://ns.electronichealth.net.au/id/hi/ihi/1.0|8003608833357361

    Implementation Notes: Fetches a bundle of all Specimen resources for the specified patient (how to search by reference and how to search by token)

Optional Search Parameters:

The following search parameter combinations SHOULD be supported:

  1. SHOULD support fetching a Specimen using the _id search parameter:
    • SHALL support these _revinclude parameters: Provenance:target GET [base]/Specimen/[id] or GET [base]/Specimen?_id=[id]

    Example:

    1. GET [base]/Specimen/2169591
    2. GET [base]/Specimen?_id=2169591
    3. GET [base]/Specimen?_id=2169591_revinclude=Provenance:target

    Implementation Notes: Fetches a single Specimen. (how to search by the logical id of the resource)