US Public Health Profiles Library
2.0.0-ballot - STU 2 - Ballot United States of America flag

This page is part of the US Public Health Profiles Library (v2.0.0-ballot: STU 2 Ballot) based on FHIR (HL7® FHIR® Standard) R4. This version is a pre-release. The current official version is 1.0.0. For a full list of available versions, see the Directory of published versions

Resource Profile: US Public Health Specimen Profile

Official URL: http://hl7.org/fhir/us/ph-library/StructureDefinition/us-ph-specimen Version: 2.0.0-ballot
Standards status: Trial-use Maturity Level: 3 Computable Name: USPublicHealthSpecimen
Other Identifiers: OID:2.16.840.1.113883.4.642.40.58.42.69

This Specimen profile represents “substances being sampled or tested. (e.g., nasopharyngeal swab, whole blood, serum, urine, wound swab)” associated with a patient related to a public health event.

It is based on the US Core Specimen Profile profile and further constrains it as follows:

  • sets the Specimen.subject to US Public Health Patient
  • constrains Specimen.identifier to Must Support
  • constrains Specimen.accessionIdentifier to Must Support
  • constrains Specimen.collection.collected[x] to Must Support
  • constrains Specimen.collection.bodySite to Must Support

Represented USCDI+ Data Elements

Use Case Data Class Data Element Name
Case Reporting Laboratory Specimen Collection Date/Time
Case Reporting Laboratory Specimen Identifier
Case Reporting Laboratory Specimen Source Site
Case Reporting Laboratory Specimen Type

Usages:

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

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

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen 0..* USCoreSpecimenProfile US Public Health Specimen Profile
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier SΣ 0..* Identifier (USCDI+) Specimen Identifier
... status ?!Σ 0..1 code available | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
... type SΣ 1..1 CodeableConcept (USCDI+) Specimen Type
Binding: SpecimenType (20240606) . (extensible)
... subject SΣ 0..1 Reference(US Public Health Patient) (USCDI) The patient where the specimen came from.
... collection 0..1 BackboneElement Collection details
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... collected[x] SΣ 0..1 (USCDI+) Specimen Collection Date/Time
..... collectedDateTime dateTime
..... collectedPeriod Period
.... bodySite S 0..1 CodeableConcept (USCDI+) Specimen Source Site
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
Specimen.statusrequiredSpecimenStatus
http://hl7.org/fhir/ValueSet/specimen-status|4.0.1
From the FHIR Standard
Specimen.typeextensibleSpecimenType .
http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54|20240606
Specimen.collection.bodySiteexampleSNOMEDCTBodyStructures
http://hl7.org/fhir/ValueSet/body-site
From the FHIR Standard

Constraints

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

This structure is derived from USCoreSpecimenProfile

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen 0..* USCoreSpecimenProfile US Public Health Specimen Profile
... identifier S 0..* Identifier (USCDI+) Specimen Identifier
... accessionIdentifier S 0..1 Identifier (USCDI+) Specimen Identifier
... type 1..1 CodeableConcept (USCDI+) Specimen Type
... collection
.... collected[x] S 0..1 dateTime, Period (USCDI+) Specimen Collection Date/Time
.... bodySite S 0..1 CodeableConcept (USCDI+) Specimen Source Site

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen 0..* USCoreSpecimenProfile US Public Health Specimen Profile
... 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
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... extension 0..* Extension Additional content defined by implementations
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier SΣ 0..* Identifier (USCDI+) Specimen Identifier
... accessionIdentifier SΣ 0..1 Identifier (USCDI+) Specimen Identifier
... status ?!Σ 0..1 code available | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
... type SΣ 1..1 CodeableConcept (USCDI+) Specimen Type
Binding: SpecimenType (20240606) . (extensible)
... subject SΣ 0..1 Reference(US Public Health Patient) (USCDI) The patient where the specimen came from.
... receivedTime Σ 0..1 dateTime The time when specimen was received for processing
... parent 0..* Reference(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] SΣ 0..1 (USCDI+) Specimen Collection Date/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: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.
.... bodySite S 0..1 CodeableConcept (USCDI+) Specimen Source Site
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
.... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
Specimen.languagepreferredCommonLanguages
http://hl7.org/fhir/ValueSet/languages
From the FHIR Standard
Additional Bindings Purpose
AllLanguages Max Binding
Specimen.statusrequiredSpecimenStatus
http://hl7.org/fhir/ValueSet/specimen-status|4.0.1
From the FHIR Standard
Specimen.typeextensibleSpecimenType .
http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54|20240606
Specimen.collection.methodexampleFHIRSpecimenCollectionMethod
http://hl7.org/fhir/ValueSet/specimen-collection-method
From the FHIR Standard
Specimen.collection.bodySiteexampleSNOMEDCTBodyStructures
http://hl7.org/fhir/ValueSet/body-site
From the FHIR Standard
Specimen.collection.fastingStatus[x]extensibleHl7VSRelevantClincialInformation
http://terminology.hl7.org/ValueSet/v2-0916
Specimen.processing.procedureexampleSpecimenProcessingProcedure
http://hl7.org/fhir/ValueSet/specimen-processing-procedure
From the FHIR Standard
Specimen.container.typeexampleSpecimenContainerType
http://hl7.org/fhir/ValueSet/specimen-container-type
From the FHIR Standard
Specimen.container.additive[x]exampleHl7VSAdditivePreservative
http://terminology.hl7.org/ValueSet/v2-0371
Specimen.conditionextensibleHl7VSSpecimenCondition
http://terminology.hl7.org/ValueSet/v2-0493

Constraints

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

This structure is derived from USCoreSpecimenProfile

Summary

Must-Support: 4 elements

Structures

This structure refers to these other structures:

Maturity: 3

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen 0..* USCoreSpecimenProfile US Public Health Specimen Profile
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier SΣ 0..* Identifier (USCDI+) Specimen Identifier
... status ?!Σ 0..1 code available | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
... type SΣ 1..1 CodeableConcept (USCDI+) Specimen Type
Binding: SpecimenType (20240606) . (extensible)
... subject SΣ 0..1 Reference(US Public Health Patient) (USCDI) The patient where the specimen came from.
... collection 0..1 BackboneElement Collection details
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... collected[x] SΣ 0..1 (USCDI+) Specimen Collection Date/Time
..... collectedDateTime dateTime
..... collectedPeriod Period
.... bodySite S 0..1 CodeableConcept (USCDI+) Specimen Source Site
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
Specimen.statusrequiredSpecimenStatus
http://hl7.org/fhir/ValueSet/specimen-status|4.0.1
From the FHIR Standard
Specimen.typeextensibleSpecimenType .
http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54|20240606
Specimen.collection.bodySiteexampleSNOMEDCTBodyStructures
http://hl7.org/fhir/ValueSet/body-site
From the FHIR Standard

Constraints

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

Differential View

This structure is derived from USCoreSpecimenProfile

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen 0..* USCoreSpecimenProfile US Public Health Specimen Profile
... identifier S 0..* Identifier (USCDI+) Specimen Identifier
... accessionIdentifier S 0..1 Identifier (USCDI+) Specimen Identifier
... type 1..1 CodeableConcept (USCDI+) Specimen Type
... collection
.... collected[x] S 0..1 dateTime, Period (USCDI+) Specimen Collection Date/Time
.... bodySite S 0..1 CodeableConcept (USCDI+) Specimen Source Site

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen 0..* USCoreSpecimenProfile US Public Health Specimen Profile
... 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
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... extension 0..* Extension Additional content defined by implementations
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier SΣ 0..* Identifier (USCDI+) Specimen Identifier
... accessionIdentifier SΣ 0..1 Identifier (USCDI+) Specimen Identifier
... status ?!Σ 0..1 code available | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
... type SΣ 1..1 CodeableConcept (USCDI+) Specimen Type
Binding: SpecimenType (20240606) . (extensible)
... subject SΣ 0..1 Reference(US Public Health Patient) (USCDI) The patient where the specimen came from.
... receivedTime Σ 0..1 dateTime The time when specimen was received for processing
... parent 0..* Reference(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] SΣ 0..1 (USCDI+) Specimen Collection Date/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: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.
.... bodySite S 0..1 CodeableConcept (USCDI+) Specimen Source Site
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
.... 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

doco Documentation for this format

Terminology Bindings

PathConformanceValueSetURI
Specimen.languagepreferredCommonLanguages
http://hl7.org/fhir/ValueSet/languages
From the FHIR Standard
Additional Bindings Purpose
AllLanguages Max Binding
Specimen.statusrequiredSpecimenStatus
http://hl7.org/fhir/ValueSet/specimen-status|4.0.1
From the FHIR Standard
Specimen.typeextensibleSpecimenType .
http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54|20240606
Specimen.collection.methodexampleFHIRSpecimenCollectionMethod
http://hl7.org/fhir/ValueSet/specimen-collection-method
From the FHIR Standard
Specimen.collection.bodySiteexampleSNOMEDCTBodyStructures
http://hl7.org/fhir/ValueSet/body-site
From the FHIR Standard
Specimen.collection.fastingStatus[x]extensibleHl7VSRelevantClincialInformation
http://terminology.hl7.org/ValueSet/v2-0916
Specimen.processing.procedureexampleSpecimenProcessingProcedure
http://hl7.org/fhir/ValueSet/specimen-processing-procedure
From the FHIR Standard
Specimen.container.typeexampleSpecimenContainerType
http://hl7.org/fhir/ValueSet/specimen-container-type
From the FHIR Standard
Specimen.container.additive[x]exampleHl7VSAdditivePreservative
http://terminology.hl7.org/ValueSet/v2-0371
Specimen.conditionextensibleHl7VSSpecimenCondition
http://terminology.hl7.org/ValueSet/v2-0493

Constraints

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

This structure is derived from USCoreSpecimenProfile

Summary

Must-Support: 4 elements

Structures

This structure refers to these other structures:

Maturity: 3

 

Other representations of profile: CSV, Excel, Schematron