This page is part of the Australian Base IG (v4.1.2-preview: AU Base) based on FHIR R4. For a full list of available versions, see the Directory of published versions

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Resource Profile: AU Base Specimen

This profile defines a specimen structure that localises core concepts, including terminology, for use in an Australian context. The purpose of this profile is to provide national level agreement on core localised concepts. This profile does not force conformance to core localised concepts. It enables implementers and modellers to make their own rules, i.e. profiling, about how to support these concepts for specific implementation needs.

Usage:

• Refer to this Resource Profile: AU Base Diagnostic Report, AU Base Diagnostic Request, AU Base Pathology Report, AU Base Pathology Result and AU Base Specimen
• Examples for this Resource Profile: Specimen/serum

Formal Views of Profile Content

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

• Differential Table
• Key Elements Table
• Snapshot Table
• Statistics/References
• All

This structure is derived from Specimen

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	A specimen in an Australian healthcare context
type		0..1	CodeableConcept	Kind of material that forms the specimen Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 (preferred)
parent		0..*	Reference(AU Base Specimen)	Specimen from which this specimen originated
collection		0..1	BackboneElement	Collection details
method		0..1	CodeableConcept	Technique used to perform collection Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 (preferred)
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (preferred)
container		0..*	BackboneElement	Direct container of specimen (tube/slide, etc.) Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-container-type-1 (preferred)
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet
Specimen.type	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1
Specimen.collection.method	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1
Specimen.collection.bodySite	preferred	https://healthterminologies.gov.au/fhir/ValueSet/body-site-1
Specimen.container	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-container-type-1

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	A specimen in an Australian healthcare context
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
status	?!Σ	0..1	code	available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
type	Σ	0..1	CodeableConcept	Kind of material that forms the specimen Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 (preferred)
parent		0..*	Reference(AU Base Specimen)	Specimen from which this specimen originated
collection		0..1	BackboneElement	Collection details
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
method		0..1	CodeableConcept	Technique used to perform collection Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 (preferred)
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (preferred)
container		0..*	BackboneElement	Direct container of specimen (tube/slide, etc.)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet
Specimen.status	required	SpecimenStatus
Specimen.type	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1
Specimen.collection.method	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1
Specimen.collection.bodySite	preferred	https://healthterminologies.gov.au/fhir/ValueSet/body-site-1

Constraints

Id	Grade	Path(s)	Details	Requirements
dom-2	error	Specimen	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Specimen	If 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-4	error	Specimen	If 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-5	error	Specimen	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Specimen	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	A specimen in an Australian healthcare context
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): A human language. Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	External Identifier
accessionIdentifier	Σ	0..1	Identifier	Identifier assigned by the lab
status	?!Σ	0..1	code	available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
type	Σ	0..1	CodeableConcept	Kind of material that forms the specimen Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 (preferred)
subject	Σ	0..1	Reference(Patient | Group | Device | Substance | Location)	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	Σ	0..1	dateTime	The time when specimen was received for processing
parent		0..*	Reference(AU Base Specimen)	Specimen from which this specimen originated
request		0..*	Reference(ServiceRequest)	Why the specimen was collected
collection		0..1	BackboneElement	Collection details
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
collector	Σ	0..1	Reference(Practitioner | PractitionerRole)	Who collected the specimen
collected[x]	Σ	0..1		Collection time
collectedDateTime			dateTime
collectedPeriod			Period
duration	Σ	0..1	Duration	How long it took to collect specimen
quantity		0..1	SimpleQuantity	The quantity of specimen collected
method		0..1	CodeableConcept	Technique used to perform collection Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 (preferred)
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (preferred)
fastingStatus[x]	Σ	0..1		Whether or how long patient abstained from food and/or drink Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.
fastingStatusCodeableConcept			CodeableConcept
fastingStatusDuration			Duration
processing		0..*	BackboneElement	Processing and processing step details
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
description		0..1	string	Textual description of procedure
procedure		0..1	CodeableConcept	Indicates 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..1		Date and time of specimen processing
timeDateTime			dateTime
timePeriod			Period
container		0..*	BackboneElement	Direct container of specimen (tube/slide, etc.)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
identifier	Σ	0..*	Identifier	Id for the container
description		0..1	string	Textual description of the container
type		0..1	CodeableConcept	Kind of container directly associated with specimen Binding: SpecimenContainerType (example): Type of specimen container.
capacity		0..1	SimpleQuantity	Container volume or size
specimenQuantity		0..1	SimpleQuantity	Quantity of specimen within container
additive[x]		0..1		Additive associated with container Binding: hl7VS-additivePreservative (example): Substance added to specimen container.
additiveCodeableConcept			CodeableConcept
additiveReference			Reference(Substance)
condition	Σ	0..*	CodeableConcept	State of the specimen Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.
note		0..*	Annotation	Comments
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet
Specimen.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding
Specimen.status	required	SpecimenStatus
Specimen.type	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1
Specimen.collection.method	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1
Specimen.collection.bodySite	preferred	https://healthterminologies.gov.au/fhir/ValueSet/body-site-1
Specimen.collection.fastingStatus[x]	extensible	Hl7VSRelevantClincialInformation
Specimen.processing.procedure	example	SpecimenProcessingProcedure
Specimen.container.type	example	SpecimenContainerType
Specimen.container.additive[x]	example	Hl7VSAdditivePreservative
Specimen.condition	extensible	Hl7VSSpecimenCondition

Constraints

Id	Grade	Path(s)	Details	Requirements
dom-2	error	Specimen	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Specimen	If 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-4	error	Specimen	If 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-5	error	Specimen	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Specimen	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

This structure is derived from Specimen

Summary

Structures

This structure refers to these other structures:

• AU Base Specimen (http://hl7.org.au/fhir/StructureDefinition/au-specimen)

Maturity: 1

Differential View

This structure is derived from Specimen

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	A specimen in an Australian healthcare context
type		0..1	CodeableConcept	Kind of material that forms the specimen Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 (preferred)
parent		0..*	Reference(AU Base Specimen)	Specimen from which this specimen originated
collection		0..1	BackboneElement	Collection details
method		0..1	CodeableConcept	Technique used to perform collection Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 (preferred)
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (preferred)
container		0..*	BackboneElement	Direct container of specimen (tube/slide, etc.) Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-container-type-1 (preferred)
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet
Specimen.type	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1
Specimen.collection.method	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1
Specimen.collection.bodySite	preferred	https://healthterminologies.gov.au/fhir/ValueSet/body-site-1
Specimen.container	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-container-type-1

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	A specimen in an Australian healthcare context
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
status	?!Σ	0..1	code	available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
type	Σ	0..1	CodeableConcept	Kind of material that forms the specimen Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 (preferred)
parent		0..*	Reference(AU Base Specimen)	Specimen from which this specimen originated
collection		0..1	BackboneElement	Collection details
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
method		0..1	CodeableConcept	Technique used to perform collection Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 (preferred)
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (preferred)
container		0..*	BackboneElement	Direct container of specimen (tube/slide, etc.)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet
Specimen.status	required	SpecimenStatus
Specimen.type	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1
Specimen.collection.method	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1
Specimen.collection.bodySite	preferred	https://healthterminologies.gov.au/fhir/ValueSet/body-site-1

Constraints

Id	Grade	Path(s)	Details	Requirements
dom-2	error	Specimen	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Specimen	If 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-4	error	Specimen	If 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-5	error	Specimen	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Specimen	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

Snapshot View

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	A specimen in an Australian healthcare context
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): A human language. Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	External Identifier
accessionIdentifier	Σ	0..1	Identifier	Identifier assigned by the lab
status	?!Σ	0..1	code	available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
type	Σ	0..1	CodeableConcept	Kind of material that forms the specimen Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 (preferred)
subject	Σ	0..1	Reference(Patient | Group | Device | Substance | Location)	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	Σ	0..1	dateTime	The time when specimen was received for processing
parent		0..*	Reference(AU Base Specimen)	Specimen from which this specimen originated
request		0..*	Reference(ServiceRequest)	Why the specimen was collected
collection		0..1	BackboneElement	Collection details
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
collector	Σ	0..1	Reference(Practitioner | PractitionerRole)	Who collected the specimen
collected[x]	Σ	0..1		Collection time
collectedDateTime			dateTime
collectedPeriod			Period
duration	Σ	0..1	Duration	How long it took to collect specimen
quantity		0..1	SimpleQuantity	The quantity of specimen collected
method		0..1	CodeableConcept	Technique used to perform collection Binding: https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 (preferred)
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 (preferred)
fastingStatus[x]	Σ	0..1		Whether or how long patient abstained from food and/or drink Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.
fastingStatusCodeableConcept			CodeableConcept
fastingStatusDuration			Duration
processing		0..*	BackboneElement	Processing and processing step details
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
description		0..1	string	Textual description of procedure
procedure		0..1	CodeableConcept	Indicates 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..1		Date and time of specimen processing
timeDateTime			dateTime
timePeriod			Period
container		0..*	BackboneElement	Direct container of specimen (tube/slide, etc.)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
identifier	Σ	0..*	Identifier	Id for the container
description		0..1	string	Textual description of the container
type		0..1	CodeableConcept	Kind of container directly associated with specimen Binding: SpecimenContainerType (example): Type of specimen container.
capacity		0..1	SimpleQuantity	Container volume or size
specimenQuantity		0..1	SimpleQuantity	Quantity of specimen within container
additive[x]		0..1		Additive associated with container Binding: hl7VS-additivePreservative (example): Substance added to specimen container.
additiveCodeableConcept			CodeableConcept
additiveReference			Reference(Substance)
condition	Σ	0..*	CodeableConcept	State of the specimen Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.
note		0..*	Annotation	Comments
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet
Specimen.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding
Specimen.status	required	SpecimenStatus
Specimen.type	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1
Specimen.collection.method	preferred	https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1
Specimen.collection.bodySite	preferred	https://healthterminologies.gov.au/fhir/ValueSet/body-site-1
Specimen.collection.fastingStatus[x]	extensible	Hl7VSRelevantClincialInformation
Specimen.processing.procedure	example	SpecimenProcessingProcedure
Specimen.container.type	example	SpecimenContainerType
Specimen.container.additive[x]	example	Hl7VSAdditivePreservative
Specimen.condition	extensible	Hl7VSSpecimenCondition

Constraints

Id	Grade	Path(s)	Details	Requirements
dom-2	error	Specimen	If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty()
dom-3	error	Specimen	If 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-4	error	Specimen	If 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-5	error	Specimen	If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty()
dom-6	best practice	Specimen	A resource should have narrative for robust management : text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both : extension.exists() != value.exists()

This structure is derived from Specimen

Summary

Structures

This structure refers to these other structures:

• AU Base Specimen (http://hl7.org.au/fhir/StructureDefinition/au-specimen)

Maturity: 1

Other representations of profile: CSV, Excel, Schematron