FHIR Implementation Guide for ABDM
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This page is part of the FHIR Implementation Guide for ABDM (v6.0.0: Release) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

Resource Profile: StructureDefinition/Specimen

Official URL: https://nrces.in/ndhm/fhir/r4/StructureDefinition/Specimen Version: 6.0.0
Draft as of 2020-08-17 Computable Name: Specimen

This profile sets minimum expectations for the Specimen resource to searching for and fetching information regarding a sample to be used for the analysis of a patient.

This profile sets minimum expectations for the Specimen resource to searching for and fetching a Organization associated with a patient or provider. It identifies which core elements, extensions, vocabularies and value sets SHALL be present in the resource when using this profile.

Examples

Usage:

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 Specimen
... type 0..1CodeableConceptKind of material that forms the specimen
Binding: Specimen Types (example)
.... coding S0..*CodingCode defined by a terminology system
..... system 1..1uriIdentity of the terminology system
Fixed Value: http://snomed.info/sct
..... code 1..1codeSymbol in syntax defined by the system
..... display 1..1stringRepresentation defined by the system
.... text S0..1stringPlain text representation of the concept
... subject 0..1Reference(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
... receivedTime S1..1dateTimeThe time when specimen was received for processing
... request 0..*Reference(ServiceRequest)Why the specimen was collected
... collection
.... collector 0..1Reference(Practitioner | PractitionerRole)Who collected the specimen
.... collected[x] 1..1dateTimeCollection time

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSetURI
Specimen.typeexampleSpecimenTypes
https://nrces.in/ndhm/fhir/r4/ValueSet/ndhm-specimen-types
from this IG
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.

.... coding SΣ0..*CodingCode defined by a terminology system
..... system Σ1..1uriIdentity of the terminology system
Fixed Value: http://snomed.info/sct
..... code Σ1..1codeSymbol in syntax defined by the system
..... display Σ1..1stringRepresentation defined by the system
.... text SΣ0..1stringPlain text representation of the concept
... subject Σ0..1Reference(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
... receivedTime SΣ1..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

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.typeexampleSpecimenTypes
https://nrces.in/ndhm/fhir/r4/ValueSet/ndhm-specimen-types
from this IG

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()
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
... 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 Σ0..1CodeableConceptKind of material that forms the specimen
Binding: Specimen Types (example)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... coding SΣ0..*CodingCode defined by a terminology system
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... system Σ1..1uriIdentity of the terminology system
Fixed Value: http://snomed.info/sct
..... version Σ0..1stringVersion of the system - if relevant
..... code Σ1..1codeSymbol in syntax defined by the system
..... display Σ1..1stringRepresentation defined by the system
..... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text SΣ0..1stringPlain text representation of the concept
... subject Σ0..1Reference(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
... receivedTime SΣ1..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] Σ1..1dateTimeCollection time
.... 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

PathConformanceValueSetURI
Specimen.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
Specimen.statusrequiredSpecimenStatus
http://hl7.org/fhir/ValueSet/specimen-status|4.0.1
from the FHIR Standard
Specimen.typeexampleSpecimenTypes
https://nrces.in/ndhm/fhir/r4/ValueSet/ndhm-specimen-types
from this IG
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()

Differential View

This structure is derived from Specimen

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen Specimen
... type 0..1CodeableConceptKind of material that forms the specimen
Binding: Specimen Types (example)
.... coding S0..*CodingCode defined by a terminology system
..... system 1..1uriIdentity of the terminology system
Fixed Value: http://snomed.info/sct
..... code 1..1codeSymbol in syntax defined by the system
..... display 1..1stringRepresentation defined by the system
.... text S0..1stringPlain text representation of the concept
... subject 0..1Reference(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
... receivedTime S1..1dateTimeThe time when specimen was received for processing
... request 0..*Reference(ServiceRequest)Why the specimen was collected
... collection
.... collector 0..1Reference(Practitioner | PractitionerRole)Who collected the specimen
.... collected[x] 1..1dateTimeCollection time

doco Documentation for this format

Terminology Bindings (Differential)

PathConformanceValueSetURI
Specimen.typeexampleSpecimenTypes
https://nrces.in/ndhm/fhir/r4/ValueSet/ndhm-specimen-types
from this IG

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.

.... coding SΣ0..*CodingCode defined by a terminology system
..... system Σ1..1uriIdentity of the terminology system
Fixed Value: http://snomed.info/sct
..... code Σ1..1codeSymbol in syntax defined by the system
..... display Σ1..1stringRepresentation defined by the system
.... text SΣ0..1stringPlain text representation of the concept
... subject Σ0..1Reference(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
... receivedTime SΣ1..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

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.typeexampleSpecimenTypes
https://nrces.in/ndhm/fhir/r4/ValueSet/ndhm-specimen-types
from this IG

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()

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
... 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 Σ0..1CodeableConceptKind of material that forms the specimen
Binding: Specimen Types (example)
.... id 0..1stringUnique id for inter-element referencing
.... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
.... coding SΣ0..*CodingCode defined by a terminology system
..... id 0..1stringUnique id for inter-element referencing
..... extension 0..*ExtensionAdditional content defined by implementations
Slice: Unordered, Open by value:url
..... system Σ1..1uriIdentity of the terminology system
Fixed Value: http://snomed.info/sct
..... version Σ0..1stringVersion of the system - if relevant
..... code Σ1..1codeSymbol in syntax defined by the system
..... display Σ1..1stringRepresentation defined by the system
..... userSelected Σ0..1booleanIf this coding was chosen directly by the user
.... text SΣ0..1stringPlain text representation of the concept
... subject Σ0..1Reference(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
... receivedTime SΣ1..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] Σ1..1dateTimeCollection time
.... 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

PathConformanceValueSetURI
Specimen.languagepreferredCommonLanguages
Additional Bindings Purpose
AllLanguages Max Binding
http://hl7.org/fhir/ValueSet/languages
from the FHIR Standard
Specimen.statusrequiredSpecimenStatus
http://hl7.org/fhir/ValueSet/specimen-status|4.0.1
from the FHIR Standard
Specimen.typeexampleSpecimenTypes
https://nrces.in/ndhm/fhir/r4/ValueSet/ndhm-specimen-types
from this IG
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()

 

Other representations of profile: CSV, Excel, Schematron