AU Base Implementation Guide
4.1.0 - Trial Use
AU Base Implementation Guide
4.1.0 - Trial Use
This page is part of the AU Base Implementation Guide 4.1.0. It is based on FHIR R4. For a full list of available versions, see the Directory of published versions
| Official URL: http://hl7.org.au/fhir/StructureDefinition/au-specimen | Version: 4.1.0 | |||
| Standards status: Trial-use | Maturity Level: 1 | Computable Name: AUBaseSpecimen | ||
Copyright/Legal: HL7 Australia© 2018+; Licensed Under Creative Commons No Rights Reserved. |
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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:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
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 | ||||
| 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 | ||||
| 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 |
| 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.
| |||||
| 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 | ||||||||
| Path | Conformance | ValueSet | ||||
| Specimen.language | preferred | CommonLanguages
| ||||
| 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 |
| Id | Grade | Path(s) | Details | Requirements |
| 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() |
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 | ||||
| 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 | ||||
| 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 |
| 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.
| |||||
| 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 | ||||||||
| Path | Conformance | ValueSet | ||||
| Specimen.language | preferred | CommonLanguages
| ||||
| 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 |
| Id | Grade | Path(s) | Details | Requirements |
| 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() |
Other representations of profile: CSV, Excel, Schematron
IG © 2017+ HL7 Australia. Package hl7.fhir.au.base#4.1.0 based on FHIR 4.0.1. Generated 2023-02-24
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