Australian Digital Health Agency FHIR Implementation Guide

Australian Digital Health Agency FHIR Implementation Guide, published by Australian Digital Health Agency. This guide is not an authorized publication; it is the continuous build for version 1.2.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/AuDigitalHealth/ci-fhir-r4/ and changes regularly. See the Directory of published versions

• Content
• Detailed Descriptions
• Examples
• XML
• JSON
• TTL

Resource Profile: ADHA Core Specimen

The purpose of this profile is to provide a core representation of a specimen for the electronic exchange of health information between individuals, healthcare providers, and the My Health Record system infrastructure in Australia. This profile supports information about a collected specimen taken from a patient for diagnostic investigation.

Usage:

• Use this Resource Profile: ADHA Core Bundle
• Refer to this Resource Profile: ADHA Pathology Result Observation
• Examples for this Resource Profile: Specimen/naso-swab-01 and Specimen/urine-01
• CapabilityStatements using this Resource Profile: ADHA Server Requirements Capability Statement

Formal Views of Profile Content

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

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

Name	Flags	Card.	Type	Description & Constraints
Specimen	C	0..*	AUBaseSpecimen	A specimen collected from a patient for the purposes of a diagnostic investigation dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources dom-3: 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 dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated dom-5: If a resource is contained in another resource, it SHALL NOT have a security label dom-6: A resource should have narrative for robust management inv-dh-spc-04: The specimen shall at least have a valid identifier or method or type
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created ele-1: All FHIR elements must have a @value or children
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
identifier	SΣC	0..*	Identifier	External Identifier ele-1: All FHIR elements must have a @value or children
accessionIdentifier	SΣC	0..1	Identifier	Identifier assigned by the lab ele-1: All FHIR elements must have a @value or children
status	?!Σ	0..1	code	available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen. ele-1: All FHIR elements must have a @value or children
type	SΣC	0..1	CodeableConcept	Kind of material that forms the specimen Binding: Specimen Type (preferred) ele-1: All FHIR elements must have a @value or children
subject	SΣC	1..1	Reference(ADHA 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 ele-1: All FHIR elements must have a @value or children inv-dh-spc-01: At least reference or a valid identifier shall be present
request	S	0..*	Reference(ADHA Core ServiceRequest)	Why the specimen was collected ele-1: All FHIR elements must have a @value or children
collection	SC	1..1	BackboneElement	Collection details ele-1: All FHIR elements must have a @value or children inv-dh-spc-02: If present, the collector shall at least have a reference or a valid identifier
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
collector	SΣC	0..1	Reference(ADHA Core PractitionerRole)	Who collected the specimen ele-1: All FHIR elements must have a @value or children
collected[x]	SΣ	1..1		Collection time ele-1: All FHIR elements must have a @value or children
collectedDateTime			dateTime
collectedPeriod			Period
method	SC	0..1	CodeableConcept	Technique used to perform collection Binding: Specimen Collection Procedure (preferred) ele-1: All FHIR elements must have a @value or children
bodySite	SC	0..1	CodeableConcept	Anatomical collection site Binding: Body Site (extensible) ele-1: All FHIR elements must have a @value or children inv-dh-spc-03: If a coded body site is provided, at least one code shall be from SNOMED CT
fastingStatus[x]	SΣ	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. ele-1: All FHIR elements must have a @value or children
fastingStatusCodeableConcept			CodeableConcept
fastingStatusDuration			Duration
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Specimen.status	required	SpecimenStatus http://hl7.org/fhir/ValueSet/specimen-status|4.0.1 from the FHIR Standard
Specimen.type	preferred	SpecimenType https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 from https://tx.ontoserver.csiro.au/fhir
Specimen.collection.method	preferred	SpecimenCollectionProcedure https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 from https://tx.ontoserver.csiro.au/fhir
Specimen.collection.bodySite	extensible	BodySite https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 from https://tx.ontoserver.csiro.au/fhir
Specimen.collection.fastingStatus[x]	extensible	Hl7VSRelevantClincialInformation http://terminology.hl7.org/ValueSet/v2-0916

Constraints

Id	Grade	Path(s)	Details	Requirements
inv-dh-spc-01	error	Specimen.subject	At least reference or a valid identifier shall be present : reference.exists() or identifier.where(system.count() + value.count() >1).exists()
inv-dh-spc-02	error	Specimen.collection	If present, the collector shall at least have a reference or a valid identifier : collector.exists() implies collector.reference.exists() or collector.identifier.where(system.count() + value.count() >1).exists()
inv-dh-spc-03	error	Specimen.collection.bodySite	If 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()
inv-dh-spc-04	error	Specimen	The 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()

This structure is derived from AUBaseSpecimen

Name	Flags	Card.	Type	Description & Constraints
Specimen	C	0..*	AUBaseSpecimen	A specimen collected from a patient for the purposes of a diagnostic investigation inv-dh-spc-04: The specimen shall at least have a valid identifier or method or type
identifier	SC	0..*	Identifier	External Identifier
accessionIdentifier	SC	0..1	Identifier	Identifier assigned by the lab
type	SC	0..1	CodeableConcept	Kind of material that forms the specimen
subject	SC	1..1	Reference(ADHA 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 inv-dh-spc-01: At least reference or a valid identifier shall be present
request	S	0..*	Reference(ADHA Core ServiceRequest)	Why the specimen was collected
collection	SC	1..1	BackboneElement	Collection details inv-dh-spc-02: If present, the collector shall at least have a reference or a valid identifier
collector	SC	0..1	Reference(ADHA Core PractitionerRole)	Who collected the specimen
collected[x]	S	1..1	dateTime, Period	Collection time
method	SC	0..1	CodeableConcept	Technique used to perform collection
bodySite	SC	0..1	CodeableConcept	Anatomical collection site Binding: Body Site (extensible) inv-dh-spc-03: If a coded body site is provided, at least one code shall be from SNOMED CT
fastingStatus[x]	S	0..1	CodeableConcept, Duration	Whether or how long patient abstained from food and/or drink
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet	URI
Specimen.collection.bodySite	extensible	BodySite https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 from https://tx.ontoserver.csiro.au/fhir

Constraints

Id	Grade	Path(s)	Details	Requirements
inv-dh-spc-01	error	Specimen.subject	At least reference or a valid identifier shall be present : reference.exists() or identifier.where(system.count() + value.count() >1).exists()
inv-dh-spc-02	error	Specimen.collection	If present, the collector shall at least have a reference or a valid identifier : collector.exists() implies collector.reference.exists() or collector.identifier.where(system.count() + value.count() >1).exists()
inv-dh-spc-03	error	Specimen.collection.bodySite	If 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()
inv-dh-spc-04	error	Specimen	The 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()

Name	Flags	Card.	Type	Description & Constraints
Specimen	C	0..*	AUBaseSpecimen	A specimen collected from a patient for the purposes of a diagnostic investigation inv-dh-spc-04: The specimen shall at least have a valid identifier or method or type
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	SΣC	0..*	Identifier	External Identifier
accessionIdentifier	SΣC	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	SΣC	0..1	CodeableConcept	Kind of material that forms the specimen Binding: Specimen Type (preferred)
subject	SΣC	1..1	Reference(ADHA 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 inv-dh-spc-01: At least reference or a valid identifier shall be present
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	S	0..*	Reference(ADHA Core ServiceRequest)	Why the specimen was collected
collection	SC	1..1	BackboneElement	Collection details inv-dh-spc-02: If present, the collector shall at least have a reference or a valid identifier
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	SΣC	0..1	Reference(ADHA Core PractitionerRole)	Who collected the specimen
collected[x]	SΣ	1..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	SC	0..1	CodeableConcept	Technique used to perform collection Binding: Specimen Collection Procedure (preferred)
bodySite	SC	0..1	CodeableConcept	Anatomical collection site Binding: Body Site (extensible) inv-dh-spc-03: If a coded body site is provided, at least one code shall be from SNOMED CT
fastingStatus[x]	SΣ	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	URI
Specimen.language	preferred	CommonLanguages http://hl7.org/fhir/ValueSet/languages from the FHIR Standard Additional Bindings Purpose AllLanguages Max Binding
Specimen.status	required	SpecimenStatus http://hl7.org/fhir/ValueSet/specimen-status|4.0.1 from the FHIR Standard
Specimen.type	preferred	SpecimenType https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 from https://tx.ontoserver.csiro.au/fhir
Specimen.collection.method	preferred	SpecimenCollectionProcedure https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 from https://tx.ontoserver.csiro.au/fhir
Specimen.collection.bodySite	extensible	BodySite https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 from https://tx.ontoserver.csiro.au/fhir
Specimen.collection.fastingStatus[x]	extensible	Hl7VSRelevantClincialInformation http://terminology.hl7.org/ValueSet/v2-0916
Specimen.processing.procedure	example	SpecimenProcessingProcedure http://hl7.org/fhir/ValueSet/specimen-processing-procedure from the FHIR Standard
Specimen.container.type	example	SpecimenContainerType http://hl7.org/fhir/ValueSet/specimen-container-type from the FHIR Standard
Specimen.container.additive[x]	example	Hl7VSAdditivePreservative http://terminology.hl7.org/ValueSet/v2-0371
Specimen.condition	extensible	Hl7VSSpecimenCondition http://terminology.hl7.org/ValueSet/v2-0493

Constraints

Id	Grade	Path(s)	Details	Requirements
inv-dh-spc-01	error	Specimen.subject	At least reference or a valid identifier shall be present : reference.exists() or identifier.where(system.count() + value.count() >1).exists()
inv-dh-spc-02	error	Specimen.collection	If present, the collector shall at least have a reference or a valid identifier : collector.exists() implies collector.reference.exists() or collector.identifier.where(system.count() + value.count() >1).exists()
inv-dh-spc-03	error	Specimen.collection.bodySite	If 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()
inv-dh-spc-04	error	Specimen	The 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()

This structure is derived from AUBaseSpecimen

Summary

Mandatory: 3 elements
Must-Support: 11 elements

Structures

This structure refers to these other structures:

• ADHA Core Patient (http://ns.electronichealth.net.au/fhir/StructureDefinition/dh-patient-core-1)
• ADHA Core ServiceRequest (http://ns.electronichealth.net.au/fhir/StructureDefinition/dh-servicerequest-core-1)
• ADHA Core PractitionerRole (http://ns.electronichealth.net.au/fhir/StructureDefinition/dh-practitionerrole-core-1)

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
Specimen	C	0..*	AUBaseSpecimen	A specimen collected from a patient for the purposes of a diagnostic investigation dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources dom-3: 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 dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated dom-5: If a resource is contained in another resource, it SHALL NOT have a security label dom-6: A resource should have narrative for robust management inv-dh-spc-04: The specimen shall at least have a valid identifier or method or type
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created ele-1: All FHIR elements must have a @value or children
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
identifier	SΣC	0..*	Identifier	External Identifier ele-1: All FHIR elements must have a @value or children
accessionIdentifier	SΣC	0..1	Identifier	Identifier assigned by the lab ele-1: All FHIR elements must have a @value or children
status	?!Σ	0..1	code	available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen. ele-1: All FHIR elements must have a @value or children
type	SΣC	0..1	CodeableConcept	Kind of material that forms the specimen Binding: Specimen Type (preferred) ele-1: All FHIR elements must have a @value or children
subject	SΣC	1..1	Reference(ADHA 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 ele-1: All FHIR elements must have a @value or children inv-dh-spc-01: At least reference or a valid identifier shall be present
request	S	0..*	Reference(ADHA Core ServiceRequest)	Why the specimen was collected ele-1: All FHIR elements must have a @value or children
collection	SC	1..1	BackboneElement	Collection details ele-1: All FHIR elements must have a @value or children inv-dh-spc-02: If present, the collector shall at least have a reference or a valid identifier
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
collector	SΣC	0..1	Reference(ADHA Core PractitionerRole)	Who collected the specimen ele-1: All FHIR elements must have a @value or children
collected[x]	SΣ	1..1		Collection time ele-1: All FHIR elements must have a @value or children
collectedDateTime			dateTime
collectedPeriod			Period
method	SC	0..1	CodeableConcept	Technique used to perform collection Binding: Specimen Collection Procedure (preferred) ele-1: All FHIR elements must have a @value or children
bodySite	SC	0..1	CodeableConcept	Anatomical collection site Binding: Body Site (extensible) ele-1: All FHIR elements must have a @value or children inv-dh-spc-03: If a coded body site is provided, at least one code shall be from SNOMED CT
fastingStatus[x]	SΣ	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. ele-1: All FHIR elements must have a @value or children
fastingStatusCodeableConcept			CodeableConcept
fastingStatusDuration			Duration
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Specimen.status	required	SpecimenStatus http://hl7.org/fhir/ValueSet/specimen-status|4.0.1 from the FHIR Standard
Specimen.type	preferred	SpecimenType https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 from https://tx.ontoserver.csiro.au/fhir
Specimen.collection.method	preferred	SpecimenCollectionProcedure https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 from https://tx.ontoserver.csiro.au/fhir
Specimen.collection.bodySite	extensible	BodySite https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 from https://tx.ontoserver.csiro.au/fhir
Specimen.collection.fastingStatus[x]	extensible	Hl7VSRelevantClincialInformation http://terminology.hl7.org/ValueSet/v2-0916

Constraints

Id	Grade	Path(s)	Details	Requirements
inv-dh-spc-01	error	Specimen.subject	At least reference or a valid identifier shall be present : reference.exists() or identifier.where(system.count() + value.count() >1).exists()
inv-dh-spc-02	error	Specimen.collection	If present, the collector shall at least have a reference or a valid identifier : collector.exists() implies collector.reference.exists() or collector.identifier.where(system.count() + value.count() >1).exists()
inv-dh-spc-03	error	Specimen.collection.bodySite	If 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()
inv-dh-spc-04	error	Specimen	The 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()

Differential View

This structure is derived from AUBaseSpecimen

Name	Flags	Card.	Type	Description & Constraints
Specimen	C	0..*	AUBaseSpecimen	A specimen collected from a patient for the purposes of a diagnostic investigation inv-dh-spc-04: The specimen shall at least have a valid identifier or method or type
identifier	SC	0..*	Identifier	External Identifier
accessionIdentifier	SC	0..1	Identifier	Identifier assigned by the lab
type	SC	0..1	CodeableConcept	Kind of material that forms the specimen
subject	SC	1..1	Reference(ADHA 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 inv-dh-spc-01: At least reference or a valid identifier shall be present
request	S	0..*	Reference(ADHA Core ServiceRequest)	Why the specimen was collected
collection	SC	1..1	BackboneElement	Collection details inv-dh-spc-02: If present, the collector shall at least have a reference or a valid identifier
collector	SC	0..1	Reference(ADHA Core PractitionerRole)	Who collected the specimen
collected[x]	S	1..1	dateTime, Period	Collection time
method	SC	0..1	CodeableConcept	Technique used to perform collection
bodySite	SC	0..1	CodeableConcept	Anatomical collection site Binding: Body Site (extensible) inv-dh-spc-03: If a coded body site is provided, at least one code shall be from SNOMED CT
fastingStatus[x]	S	0..1	CodeableConcept, Duration	Whether or how long patient abstained from food and/or drink
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet	URI
Specimen.collection.bodySite	extensible	BodySite https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 from https://tx.ontoserver.csiro.au/fhir

Constraints

Id	Grade	Path(s)	Details	Requirements
inv-dh-spc-01	error	Specimen.subject	At least reference or a valid identifier shall be present : reference.exists() or identifier.where(system.count() + value.count() >1).exists()
inv-dh-spc-02	error	Specimen.collection	If present, the collector shall at least have a reference or a valid identifier : collector.exists() implies collector.reference.exists() or collector.identifier.where(system.count() + value.count() >1).exists()
inv-dh-spc-03	error	Specimen.collection.bodySite	If 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()
inv-dh-spc-04	error	Specimen	The 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

Name	Flags	Card.	Type	Description & Constraints
Specimen	C	0..*	AUBaseSpecimen	A specimen collected from a patient for the purposes of a diagnostic investigation inv-dh-spc-04: The specimen shall at least have a valid identifier or method or type
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	SΣC	0..*	Identifier	External Identifier
accessionIdentifier	SΣC	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	SΣC	0..1	CodeableConcept	Kind of material that forms the specimen Binding: Specimen Type (preferred)
subject	SΣC	1..1	Reference(ADHA 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 inv-dh-spc-01: At least reference or a valid identifier shall be present
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	S	0..*	Reference(ADHA Core ServiceRequest)	Why the specimen was collected
collection	SC	1..1	BackboneElement	Collection details inv-dh-spc-02: If present, the collector shall at least have a reference or a valid identifier
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	SΣC	0..1	Reference(ADHA Core PractitionerRole)	Who collected the specimen
collected[x]	SΣ	1..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	SC	0..1	CodeableConcept	Technique used to perform collection Binding: Specimen Collection Procedure (preferred)
bodySite	SC	0..1	CodeableConcept	Anatomical collection site Binding: Body Site (extensible) inv-dh-spc-03: If a coded body site is provided, at least one code shall be from SNOMED CT
fastingStatus[x]	SΣ	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	URI
Specimen.language	preferred	CommonLanguages http://hl7.org/fhir/ValueSet/languages from the FHIR Standard Additional Bindings Purpose AllLanguages Max Binding
Specimen.status	required	SpecimenStatus http://hl7.org/fhir/ValueSet/specimen-status|4.0.1 from the FHIR Standard
Specimen.type	preferred	SpecimenType https://healthterminologies.gov.au/fhir/ValueSet/specimen-type-1 from https://tx.ontoserver.csiro.au/fhir
Specimen.collection.method	preferred	SpecimenCollectionProcedure https://healthterminologies.gov.au/fhir/ValueSet/specimen-collection-procedure-1 from https://tx.ontoserver.csiro.au/fhir
Specimen.collection.bodySite	extensible	BodySite https://healthterminologies.gov.au/fhir/ValueSet/body-site-1 from https://tx.ontoserver.csiro.au/fhir
Specimen.collection.fastingStatus[x]	extensible	Hl7VSRelevantClincialInformation http://terminology.hl7.org/ValueSet/v2-0916
Specimen.processing.procedure	example	SpecimenProcessingProcedure http://hl7.org/fhir/ValueSet/specimen-processing-procedure from the FHIR Standard
Specimen.container.type	example	SpecimenContainerType http://hl7.org/fhir/ValueSet/specimen-container-type from the FHIR Standard
Specimen.container.additive[x]	example	Hl7VSAdditivePreservative http://terminology.hl7.org/ValueSet/v2-0371
Specimen.condition	extensible	Hl7VSSpecimenCondition http://terminology.hl7.org/ValueSet/v2-0493

Constraints

Id	Grade	Path(s)	Details	Requirements
inv-dh-spc-01	error	Specimen.subject	At least reference or a valid identifier shall be present : reference.exists() or identifier.where(system.count() + value.count() >1).exists()
inv-dh-spc-02	error	Specimen.collection	If present, the collector shall at least have a reference or a valid identifier : collector.exists() implies collector.reference.exists() or collector.identifier.where(system.count() + value.count() >1).exists()
inv-dh-spc-03	error	Specimen.collection.bodySite	If 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()
inv-dh-spc-04	error	Specimen	The 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()

This structure is derived from AUBaseSpecimen

Summary

Mandatory: 3 elements
Must-Support: 11 elements

Structures

This structure refers to these other structures:

• ADHA Core Patient (http://ns.electronichealth.net.au/fhir/StructureDefinition/dh-patient-core-1)
• ADHA Core ServiceRequest (http://ns.electronichealth.net.au/fhir/StructureDefinition/dh-servicerequest-core-1)
• ADHA Core PractitionerRole (http://ns.electronichealth.net.au/fhir/StructureDefinition/dh-practitionerrole-core-1)

Other representations of profile: CSV, Excel, Schematron

Notes: