US Core Implementation Guide
6.0.0-ballot - STU6 Ballot US

This page is part of the US Core (v6.0.0-ballot: STU6 Ballot 1) based on FHIR R4. The current version which supercedes this version is 6.1.0. For a full list of available versions, see the Directory of published versions. Page versions: STU6.1 STU6

Resource Profile: US Core Specimen Profile

Official URL: http://hl7.org/fhir/us/core/StructureDefinition/us-core-specimen Version: 6.0.0-ballot
Active as of 2022-09-27 Computable Name: USCoreSpecimenProfile

Copyright/Legal: Used by permission of HL7 International, all rights reserved Creative Commons License

This profile sets minimum expectations for the Specimen resource to record, search, and fetch “substances being sampled or tested. (e.g., nasopharyngeal swab, whole blood, serum, urine, wound swab)” associated with a patient to promote interoperability and adoption through common implementation. It identifies which core elements, extensions, vocabularies, and value sets SHALL be present in the resource when using this profile. It provides the floor for standards development for specific use cases.

This page is new content for US Core Version 6.0.0

Example Usage Scenarios:

Queries on the Specimen resource are expected to be within the context of an Observation or DiagnosticReport resource query. The following are example usage scenarios for the US Core Specimen profile:

  • Read Specimen resources referenced in Observation resources.

Mandatory and Must Support Data Elements

The following data elements must always be present (Mandatory definition) or must be supported if the data is present in the sending system (Must Support definition). They are presented below in a simple human-readable explanation. Profile specific guidance and examples are provided as well. The Formal Views below provides the formal summary, definitions, and terminology requirements.

Each Specimen must have:

  1. A specimen code

Profile specific implementation guidance:

  • Since the binding is extensible when a code is unavailable, just text is allowed.

Usage:

  • Refer to this Resource Profile:

Formal Views of Profile Content

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

This structure is derived from Specimen

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*SpecimenSample for analysis
... type S1..1CodeableConceptKind of material that forms the specimen
Binding: VSAC 2.16.840.1.113762.1.4.1099.54 (extensible)

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSet
Specimen.typeextensiblehttp://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54
NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*SpecimenSample for analysis
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.

... type SΣ1..1CodeableConceptKind of material that forms the specimen
Binding: VSAC 2.16.840.1.113762.1.4.1099.54 (extensible)

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet
Specimen.statusrequiredSpecimenStatus
Specimen.typeextensiblehttp://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54
NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*SpecimenSample for analysis
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguagesMax Binding
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierExternal Identifier
... accessionIdentifier Σ0..1IdentifierIdentifier assigned by the lab
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.

... type SΣ1..1CodeableConceptKind of material that forms the specimen
Binding: VSAC 2.16.840.1.113762.1.4.1099.54 (extensible)
... subject Σ0..1Reference(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 Σ0..1dateTimeThe 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..1BackboneElementCollection details
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... collector Σ0..1Reference(Practitioner | PractitionerRole)Who collected the specimen
.... collected[x] Σ0..1Collection time
..... collectedDateTimedateTime
..... collectedPeriodPeriod
.... duration Σ0..1DurationHow long it took to collect specimen
.... quantity 0..1SimpleQuantityThe quantity of specimen collected
.... method 0..1CodeableConceptTechnique used to perform collection
Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.

.... bodySite 0..1CodeableConceptAnatomical collection site
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

.... fastingStatus[x] Σ0..1Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.

..... fastingStatusCodeableConceptCodeableConcept
..... fastingStatusDurationDuration
... processing 0..*BackboneElementProcessing and processing step details
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... description 0..1stringTextual description of procedure
.... procedure 0..1CodeableConceptIndicates the treatment step applied to the specimen
Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen.

.... additive 0..*Reference(Substance)Material used in the processing step
.... time[x] 0..1Date and time of specimen processing
..... timeDateTimedateTime
..... timePeriodPeriod
... container 0..*BackboneElementDirect container of specimen (tube/slide, etc.)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... identifier Σ0..*IdentifierId for the container
.... description 0..1stringTextual description of the container
.... type 0..1CodeableConceptKind of container directly associated with specimen
Binding: SpecimenContainerType (example): Type of specimen container.

.... capacity 0..1SimpleQuantityContainer volume or size
.... specimenQuantity 0..1SimpleQuantityQuantity of specimen within container
.... additive[x] 0..1Additive associated with container
Binding: hl7VS-additivePreservative (example): Substance added to specimen container.

..... additiveCodeableConceptCodeableConcept
..... additiveReferenceReference(Substance)
... condition Σ0..*CodeableConceptState of the specimen
Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.


... note 0..*AnnotationComments

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet
Specimen.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
Specimen.statusrequiredSpecimenStatus
Specimen.typeextensiblehttp://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54
Specimen.collection.methodexampleFHIRSpecimenCollectionMethod
Specimen.collection.bodySiteexampleSNOMEDCTBodyStructures
Specimen.collection.fastingStatus[x]extensibleHl7VSRelevantClincialInformation
Specimen.processing.procedureexampleSpecimenProcessingProcedure
Specimen.container.typeexampleSpecimenContainerType
Specimen.container.additive[x]exampleHl7VSAdditivePreservative
Specimen.conditionextensibleHl7VSSpecimenCondition

This structure is derived from Specimen

Summary

Mandatory: 1 element
Must-Support: 1 element

Differential View

This structure is derived from Specimen

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*SpecimenSample for analysis
... type S1..1CodeableConceptKind of material that forms the specimen
Binding: VSAC 2.16.840.1.113762.1.4.1099.54 (extensible)

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSet
Specimen.typeextensiblehttp://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54

Key Elements View

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

... type SΣ1..1CodeableConceptKind of material that forms the specimen
Binding: VSAC 2.16.840.1.113762.1.4.1099.54 (extensible)

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet
Specimen.statusrequiredSpecimenStatus
Specimen.typeextensiblehttp://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen 0..*SpecimenSample for analysis
... id Σ0..1idLogical id of this artifact
... meta Σ0..1MetaMetadata about the resource
... implicitRules ?!Σ0..1uriA set of rules under which this content was created
... language 0..1codeLanguage of the resource content
Binding: CommonLanguages (preferred): A human language.

Additional BindingsPurpose
AllLanguagesMax Binding
... text 0..1NarrativeText summary of the resource, for human interpretation
... contained 0..*ResourceContained, inline Resources
... extension 0..*ExtensionAdditional content defined by implementations
... modifierExtension ?!0..*ExtensionExtensions that cannot be ignored
... identifier Σ0..*IdentifierExternal Identifier
... accessionIdentifier Σ0..1IdentifierIdentifier assigned by the lab
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.

... type SΣ1..1CodeableConceptKind of material that forms the specimen
Binding: VSAC 2.16.840.1.113762.1.4.1099.54 (extensible)
... subject Σ0..1Reference(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 Σ0..1dateTimeThe 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..1BackboneElementCollection details
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... collector Σ0..1Reference(Practitioner | PractitionerRole)Who collected the specimen
.... collected[x] Σ0..1Collection time
..... collectedDateTimedateTime
..... collectedPeriodPeriod
.... duration Σ0..1DurationHow long it took to collect specimen
.... quantity 0..1SimpleQuantityThe quantity of specimen collected
.... method 0..1CodeableConceptTechnique used to perform collection
Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.

.... bodySite 0..1CodeableConceptAnatomical collection site
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.

.... fastingStatus[x] Σ0..1Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.

..... fastingStatusCodeableConceptCodeableConcept
..... fastingStatusDurationDuration
... processing 0..*BackboneElementProcessing and processing step details
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... description 0..1stringTextual description of procedure
.... procedure 0..1CodeableConceptIndicates the treatment step applied to the specimen
Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen.

.... additive 0..*Reference(Substance)Material used in the processing step
.... time[x] 0..1Date and time of specimen processing
..... timeDateTimedateTime
..... timePeriodPeriod
... container 0..*BackboneElementDirect container of specimen (tube/slide, etc.)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
.... modifierExtension ?!Σ0..*ExtensionExtensions that cannot be ignored even if unrecognized
.... identifier Σ0..*IdentifierId for the container
.... description 0..1stringTextual description of the container
.... type 0..1CodeableConceptKind of container directly associated with specimen
Binding: SpecimenContainerType (example): Type of specimen container.

.... capacity 0..1SimpleQuantityContainer volume or size
.... specimenQuantity 0..1SimpleQuantityQuantity of specimen within container
.... additive[x] 0..1Additive associated with container
Binding: hl7VS-additivePreservative (example): Substance added to specimen container.

..... additiveCodeableConceptCodeableConcept
..... additiveReferenceReference(Substance)
... condition Σ0..*CodeableConceptState of the specimen
Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.


... note 0..*AnnotationComments

doco Documentation for this format

Terminology Bindings

PathConformanceValueSet
Specimen.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
Specimen.statusrequiredSpecimenStatus
Specimen.typeextensiblehttp://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1099.54
Specimen.collection.methodexampleFHIRSpecimenCollectionMethod
Specimen.collection.bodySiteexampleSNOMEDCTBodyStructures
Specimen.collection.fastingStatus[x]extensibleHl7VSRelevantClincialInformation
Specimen.processing.procedureexampleSpecimenProcessingProcedure
Specimen.container.typeexampleSpecimenContainerType
Specimen.container.additive[x]exampleHl7VSAdditivePreservative
Specimen.conditionextensibleHl7VSSpecimenCondition

This structure is derived from Specimen

Summary

Mandatory: 1 element
Must-Support: 1 element

 

Other representations of profile: CSV, Excel, Schematron

Notes:


Quick Start


Below is an overview of the required Server RESTful FHIR interactions for this profile - for example, search and read operations - when supporting the US Core interactions to access this profile’s information (Profile Support + Interaction Support). Note that systems that support only US Core Profiles (Profile Only Support) are not required to support these interactions. See the US Core Server CapabilityStatement for a complete list of supported RESTful interactions for this IG.

  • The syntax used to describe the interactions is described here.
  • See the General Requirements section for additional rules and expectations when a server requires status parameters.
  • See the General Guidance section for additional guidance on searching for multiple patients.

No required search criteria for us-core-specimen profile.