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10.8 Resource Specimen - Content

Orders and Observations icon Work GroupMaturity Level: 2 Trial UseSecurity Category: Patient Compartments: Device, Patient, Practitioner

A sample to be used for analysis.

Any material sample:

  • taken from a biological entity, living or dead
  • taken from a physical object or the environment

Some specimens are biological and can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products (source: NCI Thesaurus icon, modified).

The specimen resource covers substances used for diagnostic and environmental testing. The focus of the specimen resource is the process for gathering, maintaining and processing the specimen as well as where the specimen originated. This is distinct from the use of Substance which is only used when these other aspects are not relevant.

The current definition of the specimen resource contains only basic information about specimen containers. It does not address the recursive nature of containers or the tracking of the location of a container within its parent container (for instance: a tube in a tray in a rack in a freezer). The frequency with which these elements are tracked may depend on the context of use; general lab, bio-banking, etc. Comments from reviewers on the appropriate scope for this resource, and the need for tracking related specimen management attributes, are welcomed.

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen TUDomainResourceSample for analysis

Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
... identifier Σ0..*IdentifierExternal Identifier

... accessionIdentifier Σ0..1IdentifierIdentifier assigned by the lab
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
SpecimenStatus (Required)
... subject Σ0..1Reference(Patient | Group | Device | BiologicallyDerivedProduct | 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, a biologically-derived product, or a device
... receivedTime Σ0..1dateTimeThe time when specimen is received by the testing laboratory
... parent 0..*Reference(Specimen)Specimen from which this specimen originated

... request 0..*Reference(ServiceRequest)Why the specimen was collected

... combined Σ0..1codegrouped | pooled
SpecimenCombined (Required)
... role 0..*CodeableConceptThe role the specimen serves
SpecimenRole (Preferred)

... feature 0..*BackboneElementThe physical feature of a specimen

.... type 1..1CodeableConceptHighlighted feature
SNOMED CT Body Structures (Example)
.... description 1..1stringInformation about the feature
... collection 0..1BackboneElementCollection details
.... collector Σ0..1Reference(Practitioner | PractitionerRole | Patient | RelatedPerson)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
FHIR Specimen Collection Method (Example)
.... device 0..1CodeableReference(Device)Device used to perform collection
SpecimenCollectionDevice (Example)
.... procedure 0..1Reference(Procedure)The procedure that collects the specimen
.... bodySite 0..1CodeableReference(BodyStructure)Anatomical collection site
SNOMED CT Body Structures (Example)
.... fastingStatus[x] Σ0..1Whether or how long patient abstained from food and/or drink
hl7VS-relevantClincialInformation icon (Extensible)
..... fastingStatusCodeableConceptCodeableConcept
..... fastingStatusDurationDuration
... processing 0..*BackboneElementProcessing and processing step details

.... description 0..1stringTextual description of procedure
.... method 0..1CodeableConceptIndicates the treatment step applied to the specimen
SpecimenProcessingMethod (Example)
.... 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.)

.... device 1..1Reference(Device)Device resource for the container
.... location 0..1Reference(Location)Where the container is
.... specimenQuantity 0..1SimpleQuantityQuantity of specimen within container
... condition Σ0..*CodeableConceptState of the specimen
hl7VS-specimenCondition icon (Extensible)

... note 0..*AnnotationComments


doco Documentation for this format

See the Extensions for this resource

UML Diagram (Legend)

Specimen (DomainResource)Id for specimenidentifier : Identifier [0..*]The identifier assigned by the lab when accessioning specimen(s). This is not necessarily the same as the specimen identifier, depending on local lab proceduresaccessionIdentifier : Identifier [0..1]The availability of the specimen (this element modifies the meaning of other elements)status : code [0..1] « null (Strength=Required)SpecimenStatus! »The kind of material that forms the specimentype : CodeableConcept [0..1] « null (Strength=Example)Hl7VSSpecimenType?? »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, a biologically-derived product, or a devicesubject : Reference [0..1] « Patient|Group|Device| BiologicallyDerivedProduct|Substance|Location »Time when specimen is received by the testing laboratory for processing or testingreceivedTime : dateTime [0..1]Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimenparent : Reference [0..*] « Specimen »Details concerning a service request that required a specimen to be collectedrequest : Reference [0..*] « ServiceRequest »This element signifies if the specimen is part of a group or pooledcombined : code [0..1] « null (Strength=Required)SpecimenCombined! »The role or reason for the specimen in the testing workflowrole : CodeableConcept [0..*] « null (Strength=Preferred)SpecimenRole? »A mode or state of being that describes the nature of the specimencondition : CodeableConcept [0..*] « null (Strength=Extensible)Hl7VSSpecimenCondition+ »To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen)note : Annotation [0..*]FeatureThe landmark or feature being highlightedtype : CodeableConcept [1..1] « null (Strength=Example)SNOMEDCTBodyStructures?? »Description of the feature of the specimendescription : string [1..1]CollectionPerson who collected the specimencollector : Reference [0..1] « Practitioner|PractitionerRole|Patient| RelatedPerson »Time when specimen was collected from subject - the physiologically relevant timecollected[x] : DataType [0..1] « dateTime|Period »The span of time over which the collection of a specimen occurredduration : Duration [0..1]The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology samplequantity : Quantity(SimpleQuantity) [0..1]A coded value specifying the technique that is used to perform the proceduremethod : CodeableConcept [0..1] « null (Strength=Example)FHIRSpecimenCollectionMethod?? »A coded value specifying the technique that is used to perform the proceduredevice : CodeableReference [0..1] « Device; null (Strength=Example)SpecimenCollectionDevice?? »The procedure event during which the specimen was collected (e.g. the surgery leading to the collection of a pathology sample)procedure : Reference [0..1] « Procedure »Anatomical location from which the specimen was collected (if subject is a patient). This is the target site. This element is not used for environmental specimensbodySite : CodeableReference [0..1] « BodyStructure; null (Strength=Example) SNOMEDCTBodyStructures?? »Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collectionfastingStatus[x] : DataType [0..1] « CodeableConcept|Duration; null (Strength=Extensible) Hl7VSRelevantClincialInformat...+ »ProcessingTextual description of proceduredescription : string [0..1]A coded value specifying the method used to process the specimenmethod : CodeableConcept [0..1] « null (Strength=Example)SpecimenProcessingMethod?? »Material used in the processing stepadditive : Reference [0..*] « Substance »A record of the time or period when the specimen processing occurred. For example the time of sample fixation or the period of time the sample was in formalintime[x] : DataType [0..1] « dateTime|Period »ContainerThe device resource for the the container holding the specimen. If the container is in a holder then the referenced device will point to a parent devicedevice : Reference [1..1] « Device »The location of the container holding the specimenlocation : Reference [0..1] « Location »The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen typespecimenQuantity : Quantity(SimpleQuantity) [0..1]A physical feature or landmark on a specimen, highlighted for context by the collector of the specimen (e.g. surgeon), that identifies the type of feature as well as its meaning (e.g. the red ink indicating the resection margin of the right lobe of the excised prostate tissue or wire loop at radiologically suspected tumor location)feature[0..*]Details concerning the specimen collectioncollection[0..1]Details concerning processing and processing steps for the specimenprocessing[0..*]The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed herecontainer[0..*]

XML Template

<Specimen xmlns="http://hl7.org/fhir"> doco
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <identifier><!-- 0..* Identifier External Identifier --></identifier>
 <accessionIdentifier><!-- 0..1 Identifier Identifier assigned by the lab --></accessionIdentifier>
 <status value="[code]"/><!-- 0..1 available | unavailable | unsatisfactory | entered-in-error -->
 <type><!-- 0..1 CodeableConcept Kind of material that forms the specimen icon --></type>
 <subject><!-- 0..1 Reference(BiologicallyDerivedProduct|Device|Group|Location|
   Patient|Substance) 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, a biologically-derived product, or a device --></subject>
 <receivedTime value="[dateTime]"/><!-- 0..1 The time when specimen is received by the testing laboratory -->
 <parent><!-- 0..* Reference(Specimen) Specimen from which this specimen originated --></parent>
 <request><!-- 0..* Reference(ServiceRequest) Why the specimen was collected --></request>
 <combined value="[code]"/><!-- 0..1 grouped | pooled -->
 <role><!-- 0..* CodeableConcept The role the specimen serves --></role>
 <feature>  <!-- 0..* The physical feature of a specimen  -->
  <type><!-- 1..1 CodeableConcept Highlighted feature --></type>
  <description value="[string]"/><!-- 1..1 Information about the feature -->
 </feature>
 <collection>  <!-- 0..1 Collection details -->
  <collector><!-- 0..1 Reference(Patient|Practitioner|PractitionerRole|
    RelatedPerson) Who collected the specimen --></collector>
  <collected[x]><!-- 0..1 dateTime|Period Collection time --></collected[x]>
  <duration><!-- 0..1 Duration How long it took to collect specimen --></duration>
  <quantity><!-- 0..1 Quantity(SimpleQuantity) The quantity of specimen collected --></quantity>
  <method><!-- 0..1 CodeableConcept Technique used to perform collection --></method>
  <device><!-- 0..1 CodeableReference(Device) Device used to perform collection --></device>
  <procedure><!-- 0..1 Reference(Procedure) The procedure that collects the specimen --></procedure>
  <bodySite><!-- 0..1 CodeableReference(BodyStructure) Anatomical collection site --></bodySite>
  <fastingStatus[x]><!-- 0..1 CodeableConcept|Duration Whether or how long patient abstained from food and/or drink icon --></fastingStatus[x]>
 </collection>
 <processing>  <!-- 0..* Processing and processing step details -->
  <description value="[string]"/><!-- 0..1 Textual description of procedure -->
  <method><!-- 0..1 CodeableConcept Indicates the treatment step  applied to the specimen --></method>
  <additive><!-- 0..* Reference(Substance) Material used in the processing step --></additive>
  <time[x]><!-- 0..1 dateTime|Period Date and time of specimen processing --></time[x]>
 </processing>
 <container>  <!-- 0..* Direct container of specimen (tube/slide, etc.) -->
  <device><!-- 1..1 Reference(Device) Device resource for the container --></device>
  <location><!-- 0..1 Reference(Location) Where the container is --></location>
  <specimenQuantity><!-- 0..1 Quantity(SimpleQuantity) Quantity of specimen within container --></specimenQuantity>
 </container>
 <condition><!-- 0..* CodeableConcept State of the specimen icon --></condition>
 <note><!-- 0..* Annotation Comments --></note>
</Specimen>

JSON Template

{doco
  "resourceType" : "Specimen",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // External Identifier
  "accessionIdentifier" : { Identifier }, // Identifier assigned by the lab
  "status" : "<code>", // available | unavailable | unsatisfactory | entered-in-error
  "type" : { CodeableConcept }, // Kind of material that forms the specimen icon
  "subject" : { Reference(BiologicallyDerivedProduct|Device|Group|Location|
   Patient|Substance) }, // 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, a biologically-derived product, or a device
  "receivedTime" : "<dateTime>", // The time when specimen is received by the testing laboratory
  "parent" : [{ Reference(Specimen) }], // Specimen from which this specimen originated
  "request" : [{ Reference(ServiceRequest) }], // Why the specimen was collected
  "combined" : "<code>", // grouped | pooled
  "role" : [{ CodeableConcept }], // The role the specimen serves
  "feature" : [{ // The physical feature of a specimen 
    "type" : { CodeableConcept }, // R!  Highlighted feature
    "description" : "<string>" // R!  Information about the feature
  }],
  "collection" : { // Collection details
    "collector" : { Reference(Patient|Practitioner|PractitionerRole|
    RelatedPerson) }, // Who collected the specimen
    // collected[x]: Collection time. One of these 2:
    "collectedDateTime" : "<dateTime>",
    "collectedPeriod" : { Period },
    "duration" : { Duration }, // How long it took to collect specimen
    "quantity" : { Quantity(SimpleQuantity) }, // The quantity of specimen collected
    "method" : { CodeableConcept }, // Technique used to perform collection
    "device" : { CodeableReference(Device) }, // Device used to perform collection
    "procedure" : { Reference(Procedure) }, // The procedure that collects the specimen
    "bodySite" : { CodeableReference(BodyStructure) }, // Anatomical collection site
    // fastingStatus[x]: Whether or how long patient abstained from food and/or drink. One of these 2:
    "fastingStatusCodeableConcept" : { CodeableConcept },
    "fastingStatusDuration" : { Duration }
  },
  "processing" : [{ // Processing and processing step details
    "description" : "<string>", // Textual description of procedure
    "method" : { CodeableConcept }, // Indicates the treatment step  applied to the specimen
    "additive" : [{ Reference(Substance) }], // Material used in the processing step
    // time[x]: Date and time of specimen processing. One of these 2:
    "timeDateTime" : "<dateTime>",
    "timePeriod" : { Period }
  }],
  "container" : [{ // Direct container of specimen (tube/slide, etc.)
    "device" : { Reference(Device) }, // R!  Device resource for the container
    "location" : { Reference(Location) }, // Where the container is
    "specimenQuantity" : { Quantity(SimpleQuantity) } // Quantity of specimen within container
  }],
  "condition" : [{ CodeableConcept }], // State of the specimen icon
  "note" : [{ Annotation }] // Comments
}

Turtle Template

@prefix fhir: <http://hl7.org/fhir/> .doco


[ a fhir:Specimen;
  fhir:nodeRole fhir:treeRoot; # if this is the parser root

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:Specimen.identifier [ Identifier ], ... ; # 0..* External Identifier
  fhir:Specimen.accessionIdentifier [ Identifier ]; # 0..1 Identifier assigned by the lab
  fhir:Specimen.status [ code ]; # 0..1 available | unavailable | unsatisfactory | entered-in-error
  fhir:Specimen.type [ CodeableConcept ]; # 0..1 Kind of material that forms the specimen
  fhir:Specimen.subject [ Reference(BiologicallyDerivedProduct|Device|Group|Location|Patient|Substance) ]; # 0..1 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, a biologically-derived product, or a device
  fhir:Specimen.receivedTime [ dateTime ]; # 0..1 The time when specimen is received by the testing laboratory
  fhir:Specimen.parent [ Reference(Specimen) ], ... ; # 0..* Specimen from which this specimen originated
  fhir:Specimen.request [ Reference(ServiceRequest) ], ... ; # 0..* Why the specimen was collected
  fhir:Specimen.combined [ code ]; # 0..1 grouped | pooled
  fhir:Specimen.role [ CodeableConcept ], ... ; # 0..* The role the specimen serves
  fhir:Specimen.feature [ # 0..* The physical feature of a specimen 
    fhir:Specimen.feature.type [ CodeableConcept ]; # 1..1 Highlighted feature
    fhir:Specimen.feature.description [ string ]; # 1..1 Information about the feature
  ], ...;
  fhir:Specimen.collection [ # 0..1 Collection details
    fhir:Specimen.collection.collector [ Reference(Patient|Practitioner|PractitionerRole|RelatedPerson) ]; # 0..1 Who collected the specimen
    # Specimen.collection.collected[x] : 0..1 Collection time. One of these 2
      fhir:Specimen.collection.collectedDateTime [ dateTime ]
      fhir:Specimen.collection.collectedPeriod [ Period ]
    fhir:Specimen.collection.duration [ Duration ]; # 0..1 How long it took to collect specimen
    fhir:Specimen.collection.quantity [ Quantity(SimpleQuantity) ]; # 0..1 The quantity of specimen collected
    fhir:Specimen.collection.method [ CodeableConcept ]; # 0..1 Technique used to perform collection
    fhir:Specimen.collection.device [ CodeableReference(Device) ]; # 0..1 Device used to perform collection
    fhir:Specimen.collection.procedure [ Reference(Procedure) ]; # 0..1 The procedure that collects the specimen
    fhir:Specimen.collection.bodySite [ CodeableReference(BodyStructure) ]; # 0..1 Anatomical collection site
    # Specimen.collection.fastingStatus[x] : 0..1 Whether or how long patient abstained from food and/or drink. One of these 2
      fhir:Specimen.collection.fastingStatusCodeableConcept [ CodeableConcept ]
      fhir:Specimen.collection.fastingStatusDuration [ Duration ]
  ];
  fhir:Specimen.processing [ # 0..* Processing and processing step details
    fhir:Specimen.processing.description [ string ]; # 0..1 Textual description of procedure
    fhir:Specimen.processing.method [ CodeableConcept ]; # 0..1 Indicates the treatment step  applied to the specimen
    fhir:Specimen.processing.additive [ Reference(Substance) ], ... ; # 0..* Material used in the processing step
    # Specimen.processing.time[x] : 0..1 Date and time of specimen processing. One of these 2
      fhir:Specimen.processing.timeDateTime [ dateTime ]
      fhir:Specimen.processing.timePeriod [ Period ]
  ], ...;
  fhir:Specimen.container [ # 0..* Direct container of specimen (tube/slide, etc.)
    fhir:Specimen.container.device [ Reference(Device) ]; # 1..1 Device resource for the container
    fhir:Specimen.container.location [ Reference(Location) ]; # 0..1 Where the container is
    fhir:Specimen.container.specimenQuantity [ Quantity(SimpleQuantity) ]; # 0..1 Quantity of specimen within container
  ], ...;
  fhir:Specimen.condition [ CodeableConcept ], ... ; # 0..* State of the specimen
  fhir:Specimen.note [ Annotation ], ... ; # 0..* Comments
]

Changes since R4

Specimen
Specimen.subject
  • Type Reference: Added Target Type BiologicallyDerivedProduct
  • Type Reference: Added Target Type BiologicallyDerivedProduct
Specimen.combined
  • Added Element
Specimen.role
  • Added Element
Specimen.feature
  • Added Element
Specimen.feature.type
  • Added Mandatory Element
Specimen.feature.description
  • Added Mandatory Element
Specimen.collection.collector
  • Type Reference: Added Target Types Patient, RelatedPerson
  • Type Reference: Added Target Types Patient, RelatedPerson
Specimen.collection.device
  • Added Element
Specimen.collection.procedure
  • Added Element
Specimen.collection.bodySite
  • Type changed from CodeableConcept to CodeableReference
  • Type changed from CodeableConcept to CodeableReference
Specimen.processing.method
  • Added Element
Specimen.container.device
  • Added Mandatory Element
Specimen.container.location
  • Added Element
Specimen.processing.procedure
  • deleted
Specimen.container.identifier
  • deleted
Specimen.container.description
  • deleted
Specimen.container.type
  • deleted
Specimen.container.capacity
  • deleted
Specimen.container.additive[x]
  • deleted

See the Full Difference for further information

This analysis is available as XML or JSON.

See R3 <--> R4 Conversion Maps (status = 4 tests that all execute ok. All tests pass round-trip testing and 2 r3 resources are invalid (0 errors).)

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen TUDomainResourceSample for analysis

Elements defined in Ancestors: id, meta, implicitRules, language, text, contained, extension, modifierExtension
... identifier Σ0..*IdentifierExternal Identifier

... accessionIdentifier Σ0..1IdentifierIdentifier assigned by the lab
... status ?!Σ0..1codeavailable | unavailable | unsatisfactory | entered-in-error
SpecimenStatus (Required)
... subject Σ0..1Reference(Patient | Group | Device | BiologicallyDerivedProduct | 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, a biologically-derived product, or a device
... receivedTime Σ0..1dateTimeThe time when specimen is received by the testing laboratory
... parent 0..*Reference(Specimen)Specimen from which this specimen originated

... request 0..*Reference(ServiceRequest)Why the specimen was collected

... combined Σ0..1codegrouped | pooled
SpecimenCombined (Required)
... role 0..*CodeableConceptThe role the specimen serves
SpecimenRole (Preferred)

... feature 0..*BackboneElementThe physical feature of a specimen

.... type 1..1CodeableConceptHighlighted feature
SNOMED CT Body Structures (Example)
.... description 1..1stringInformation about the feature
... collection 0..1BackboneElementCollection details
.... collector Σ0..1Reference(Practitioner | PractitionerRole | Patient | RelatedPerson)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
FHIR Specimen Collection Method (Example)
.... device 0..1CodeableReference(Device)Device used to perform collection
SpecimenCollectionDevice (Example)
.... procedure 0..1Reference(Procedure)The procedure that collects the specimen
.... bodySite 0..1CodeableReference(BodyStructure)Anatomical collection site
SNOMED CT Body Structures (Example)
.... fastingStatus[x] Σ0..1Whether or how long patient abstained from food and/or drink
hl7VS-relevantClincialInformation icon (Extensible)
..... fastingStatusCodeableConceptCodeableConcept
..... fastingStatusDurationDuration
... processing 0..*BackboneElementProcessing and processing step details

.... description 0..1stringTextual description of procedure
.... method 0..1CodeableConceptIndicates the treatment step applied to the specimen
SpecimenProcessingMethod (Example)
.... 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.)

.... device 1..1Reference(Device)Device resource for the container
.... location 0..1Reference(Location)Where the container is
.... specimenQuantity 0..1SimpleQuantityQuantity of specimen within container
... condition Σ0..*CodeableConceptState of the specimen
hl7VS-specimenCondition icon (Extensible)

... note 0..*AnnotationComments


doco Documentation for this format

See the Extensions for this resource

UML Diagram (Legend)

Specimen (DomainResource)Id for specimenidentifier : Identifier [0..*]The identifier assigned by the lab when accessioning specimen(s). This is not necessarily the same as the specimen identifier, depending on local lab proceduresaccessionIdentifier : Identifier [0..1]The availability of the specimen (this element modifies the meaning of other elements)status : code [0..1] « null (Strength=Required)SpecimenStatus! »The kind of material that forms the specimentype : CodeableConcept [0..1] « null (Strength=Example)Hl7VSSpecimenType?? »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, a biologically-derived product, or a devicesubject : Reference [0..1] « Patient|Group|Device| BiologicallyDerivedProduct|Substance|Location »Time when specimen is received by the testing laboratory for processing or testingreceivedTime : dateTime [0..1]Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimenparent : Reference [0..*] « Specimen »Details concerning a service request that required a specimen to be collectedrequest : Reference [0..*] « ServiceRequest »This element signifies if the specimen is part of a group or pooledcombined : code [0..1] « null (Strength=Required)SpecimenCombined! »The role or reason for the specimen in the testing workflowrole : CodeableConcept [0..*] « null (Strength=Preferred)SpecimenRole? »A mode or state of being that describes the nature of the specimencondition : CodeableConcept [0..*] « null (Strength=Extensible)Hl7VSSpecimenCondition+ »To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen)note : Annotation [0..*]FeatureThe landmark or feature being highlightedtype : CodeableConcept [1..1] « null (Strength=Example)SNOMEDCTBodyStructures?? »Description of the feature of the specimendescription : string [1..1]CollectionPerson who collected the specimencollector : Reference [0..1] « Practitioner|PractitionerRole|Patient| RelatedPerson »Time when specimen was collected from subject - the physiologically relevant timecollected[x] : DataType [0..1] « dateTime|Period »The span of time over which the collection of a specimen occurredduration : Duration [0..1]The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology samplequantity : Quantity(SimpleQuantity) [0..1]A coded value specifying the technique that is used to perform the proceduremethod : CodeableConcept [0..1] « null (Strength=Example)FHIRSpecimenCollectionMethod?? »A coded value specifying the technique that is used to perform the proceduredevice : CodeableReference [0..1] « Device; null (Strength=Example)SpecimenCollectionDevice?? »The procedure event during which the specimen was collected (e.g. the surgery leading to the collection of a pathology sample)procedure : Reference [0..1] « Procedure »Anatomical location from which the specimen was collected (if subject is a patient). This is the target site. This element is not used for environmental specimensbodySite : CodeableReference [0..1] « BodyStructure; null (Strength=Example) SNOMEDCTBodyStructures?? »Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collectionfastingStatus[x] : DataType [0..1] « CodeableConcept|Duration; null (Strength=Extensible) Hl7VSRelevantClincialInformat...+ »ProcessingTextual description of proceduredescription : string [0..1]A coded value specifying the method used to process the specimenmethod : CodeableConcept [0..1] « null (Strength=Example)SpecimenProcessingMethod?? »Material used in the processing stepadditive : Reference [0..*] « Substance »A record of the time or period when the specimen processing occurred. For example the time of sample fixation or the period of time the sample was in formalintime[x] : DataType [0..1] « dateTime|Period »ContainerThe device resource for the the container holding the specimen. If the container is in a holder then the referenced device will point to a parent devicedevice : Reference [1..1] « Device »The location of the container holding the specimenlocation : Reference [0..1] « Location »The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen typespecimenQuantity : Quantity(SimpleQuantity) [0..1]A physical feature or landmark on a specimen, highlighted for context by the collector of the specimen (e.g. surgeon), that identifies the type of feature as well as its meaning (e.g. the red ink indicating the resection margin of the right lobe of the excised prostate tissue or wire loop at radiologically suspected tumor location)feature[0..*]Details concerning the specimen collectioncollection[0..1]Details concerning processing and processing steps for the specimenprocessing[0..*]The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed herecontainer[0..*]

XML Template

<Specimen xmlns="http://hl7.org/fhir"> doco
 <!-- from Resource: id, meta, implicitRules, and language -->
 <!-- from DomainResource: text, contained, extension, and modifierExtension -->
 <identifier><!-- 0..* Identifier External Identifier --></identifier>
 <accessionIdentifier><!-- 0..1 Identifier Identifier assigned by the lab --></accessionIdentifier>
 <status value="[code]"/><!-- 0..1 available | unavailable | unsatisfactory | entered-in-error -->
 <type><!-- 0..1 CodeableConcept Kind of material that forms the specimen icon --></type>
 <subject><!-- 0..1 Reference(BiologicallyDerivedProduct|Device|Group|Location|
   Patient|Substance) 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, a biologically-derived product, or a device --></subject>
 <receivedTime value="[dateTime]"/><!-- 0..1 The time when specimen is received by the testing laboratory -->
 <parent><!-- 0..* Reference(Specimen) Specimen from which this specimen originated --></parent>
 <request><!-- 0..* Reference(ServiceRequest) Why the specimen was collected --></request>
 <combined value="[code]"/><!-- 0..1 grouped | pooled -->
 <role><!-- 0..* CodeableConcept The role the specimen serves --></role>
 <feature>  <!-- 0..* The physical feature of a specimen  -->
  <type><!-- 1..1 CodeableConcept Highlighted feature --></type>
  <description value="[string]"/><!-- 1..1 Information about the feature -->
 </feature>
 <collection>  <!-- 0..1 Collection details -->
  <collector><!-- 0..1 Reference(Patient|Practitioner|PractitionerRole|
    RelatedPerson) Who collected the specimen --></collector>
  <collected[x]><!-- 0..1 dateTime|Period Collection time --></collected[x]>
  <duration><!-- 0..1 Duration How long it took to collect specimen --></duration>
  <quantity><!-- 0..1 Quantity(SimpleQuantity) The quantity of specimen collected --></quantity>
  <method><!-- 0..1 CodeableConcept Technique used to perform collection --></method>
  <device><!-- 0..1 CodeableReference(Device) Device used to perform collection --></device>
  <procedure><!-- 0..1 Reference(Procedure) The procedure that collects the specimen --></procedure>
  <bodySite><!-- 0..1 CodeableReference(BodyStructure) Anatomical collection site --></bodySite>
  <fastingStatus[x]><!-- 0..1 CodeableConcept|Duration Whether or how long patient abstained from food and/or drink icon --></fastingStatus[x]>
 </collection>
 <processing>  <!-- 0..* Processing and processing step details -->
  <description value="[string]"/><!-- 0..1 Textual description of procedure -->
  <method><!-- 0..1 CodeableConcept Indicates the treatment step  applied to the specimen --></method>
  <additive><!-- 0..* Reference(Substance) Material used in the processing step --></additive>
  <time[x]><!-- 0..1 dateTime|Period Date and time of specimen processing --></time[x]>
 </processing>
 <container>  <!-- 0..* Direct container of specimen (tube/slide, etc.) -->
  <device><!-- 1..1 Reference(Device) Device resource for the container --></device>
  <location><!-- 0..1 Reference(Location) Where the container is --></location>
  <specimenQuantity><!-- 0..1 Quantity(SimpleQuantity) Quantity of specimen within container --></specimenQuantity>
 </container>
 <condition><!-- 0..* CodeableConcept State of the specimen icon --></condition>
 <note><!-- 0..* Annotation Comments --></note>
</Specimen>

JSON Template

{doco
  "resourceType" : "Specimen",
  // from Resource: id, meta, implicitRules, and language
  // from DomainResource: text, contained, extension, and modifierExtension
  "identifier" : [{ Identifier }], // External Identifier
  "accessionIdentifier" : { Identifier }, // Identifier assigned by the lab
  "status" : "<code>", // available | unavailable | unsatisfactory | entered-in-error
  "type" : { CodeableConcept }, // Kind of material that forms the specimen icon
  "subject" : { Reference(BiologicallyDerivedProduct|Device|Group|Location|
   Patient|Substance) }, // 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, a biologically-derived product, or a device
  "receivedTime" : "<dateTime>", // The time when specimen is received by the testing laboratory
  "parent" : [{ Reference(Specimen) }], // Specimen from which this specimen originated
  "request" : [{ Reference(ServiceRequest) }], // Why the specimen was collected
  "combined" : "<code>", // grouped | pooled
  "role" : [{ CodeableConcept }], // The role the specimen serves
  "feature" : [{ // The physical feature of a specimen 
    "type" : { CodeableConcept }, // R!  Highlighted feature
    "description" : "<string>" // R!  Information about the feature
  }],
  "collection" : { // Collection details
    "collector" : { Reference(Patient|Practitioner|PractitionerRole|
    RelatedPerson) }, // Who collected the specimen
    // collected[x]: Collection time. One of these 2:
    "collectedDateTime" : "<dateTime>",
    "collectedPeriod" : { Period },
    "duration" : { Duration }, // How long it took to collect specimen
    "quantity" : { Quantity(SimpleQuantity) }, // The quantity of specimen collected
    "method" : { CodeableConcept }, // Technique used to perform collection
    "device" : { CodeableReference(Device) }, // Device used to perform collection
    "procedure" : { Reference(Procedure) }, // The procedure that collects the specimen
    "bodySite" : { CodeableReference(BodyStructure) }, // Anatomical collection site
    // fastingStatus[x]: Whether or how long patient abstained from food and/or drink. One of these 2:
    "fastingStatusCodeableConcept" : { CodeableConcept },
    "fastingStatusDuration" : { Duration }
  },
  "processing" : [{ // Processing and processing step details
    "description" : "<string>", // Textual description of procedure
    "method" : { CodeableConcept }, // Indicates the treatment step  applied to the specimen
    "additive" : [{ Reference(Substance) }], // Material used in the processing step
    // time[x]: Date and time of specimen processing. One of these 2:
    "timeDateTime" : "<dateTime>",
    "timePeriod" : { Period }
  }],
  "container" : [{ // Direct container of specimen (tube/slide, etc.)
    "device" : { Reference(Device) }, // R!  Device resource for the container
    "location" : { Reference(Location) }, // Where the container is
    "specimenQuantity" : { Quantity(SimpleQuantity) } // Quantity of specimen within container
  }],
  "condition" : [{ CodeableConcept }], // State of the specimen icon
  "note" : [{ Annotation }] // Comments
}

Turtle Template

@prefix fhir: <http://hl7.org/fhir/> .doco


[ a fhir:Specimen;
  fhir:nodeRole fhir:treeRoot; # if this is the parser root

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:Specimen.identifier [ Identifier ], ... ; # 0..* External Identifier
  fhir:Specimen.accessionIdentifier [ Identifier ]; # 0..1 Identifier assigned by the lab
  fhir:Specimen.status [ code ]; # 0..1 available | unavailable | unsatisfactory | entered-in-error
  fhir:Specimen.type [ CodeableConcept ]; # 0..1 Kind of material that forms the specimen
  fhir:Specimen.subject [ Reference(BiologicallyDerivedProduct|Device|Group|Location|Patient|Substance) ]; # 0..1 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, a biologically-derived product, or a device
  fhir:Specimen.receivedTime [ dateTime ]; # 0..1 The time when specimen is received by the testing laboratory
  fhir:Specimen.parent [ Reference(Specimen) ], ... ; # 0..* Specimen from which this specimen originated
  fhir:Specimen.request [ Reference(ServiceRequest) ], ... ; # 0..* Why the specimen was collected
  fhir:Specimen.combined [ code ]; # 0..1 grouped | pooled
  fhir:Specimen.role [ CodeableConcept ], ... ; # 0..* The role the specimen serves
  fhir:Specimen.feature [ # 0..* The physical feature of a specimen 
    fhir:Specimen.feature.type [ CodeableConcept ]; # 1..1 Highlighted feature
    fhir:Specimen.feature.description [ string ]; # 1..1 Information about the feature
  ], ...;
  fhir:Specimen.collection [ # 0..1 Collection details
    fhir:Specimen.collection.collector [ Reference(Patient|Practitioner|PractitionerRole|RelatedPerson) ]; # 0..1 Who collected the specimen
    # Specimen.collection.collected[x] : 0..1 Collection time. One of these 2
      fhir:Specimen.collection.collectedDateTime [ dateTime ]
      fhir:Specimen.collection.collectedPeriod [ Period ]
    fhir:Specimen.collection.duration [ Duration ]; # 0..1 How long it took to collect specimen
    fhir:Specimen.collection.quantity [ Quantity(SimpleQuantity) ]; # 0..1 The quantity of specimen collected
    fhir:Specimen.collection.method [ CodeableConcept ]; # 0..1 Technique used to perform collection
    fhir:Specimen.collection.device [ CodeableReference(Device) ]; # 0..1 Device used to perform collection
    fhir:Specimen.collection.procedure [ Reference(Procedure) ]; # 0..1 The procedure that collects the specimen
    fhir:Specimen.collection.bodySite [ CodeableReference(BodyStructure) ]; # 0..1 Anatomical collection site
    # Specimen.collection.fastingStatus[x] : 0..1 Whether or how long patient abstained from food and/or drink. One of these 2
      fhir:Specimen.collection.fastingStatusCodeableConcept [ CodeableConcept ]
      fhir:Specimen.collection.fastingStatusDuration [ Duration ]
  ];
  fhir:Specimen.processing [ # 0..* Processing and processing step details
    fhir:Specimen.processing.description [ string ]; # 0..1 Textual description of procedure
    fhir:Specimen.processing.method [ CodeableConcept ]; # 0..1 Indicates the treatment step  applied to the specimen
    fhir:Specimen.processing.additive [ Reference(Substance) ], ... ; # 0..* Material used in the processing step
    # Specimen.processing.time[x] : 0..1 Date and time of specimen processing. One of these 2
      fhir:Specimen.processing.timeDateTime [ dateTime ]
      fhir:Specimen.processing.timePeriod [ Period ]
  ], ...;
  fhir:Specimen.container [ # 0..* Direct container of specimen (tube/slide, etc.)
    fhir:Specimen.container.device [ Reference(Device) ]; # 1..1 Device resource for the container
    fhir:Specimen.container.location [ Reference(Location) ]; # 0..1 Where the container is
    fhir:Specimen.container.specimenQuantity [ Quantity(SimpleQuantity) ]; # 0..1 Quantity of specimen within container
  ], ...;
  fhir:Specimen.condition [ CodeableConcept ], ... ; # 0..* State of the specimen
  fhir:Specimen.note [ Annotation ], ... ; # 0..* Comments
]

Changes since Release 4

Specimen
Specimen.subject
  • Type Reference: Added Target Type BiologicallyDerivedProduct
  • Type Reference: Added Target Type BiologicallyDerivedProduct
Specimen.combined
  • Added Element
Specimen.role
  • Added Element
Specimen.feature
  • Added Element
Specimen.feature.type
  • Added Mandatory Element
Specimen.feature.description
  • Added Mandatory Element
Specimen.collection.collector
  • Type Reference: Added Target Types Patient, RelatedPerson
  • Type Reference: Added Target Types Patient, RelatedPerson
Specimen.collection.device
  • Added Element
Specimen.collection.procedure
  • Added Element
Specimen.collection.bodySite
  • Type changed from CodeableConcept to CodeableReference
  • Type changed from CodeableConcept to CodeableReference
Specimen.processing.method
  • Added Element
Specimen.container.device
  • Added Mandatory Element
Specimen.container.location
  • Added Element
Specimen.processing.procedure
  • deleted
Specimen.container.identifier
  • deleted
Specimen.container.description
  • deleted
Specimen.container.type
  • deleted
Specimen.container.capacity
  • deleted
Specimen.container.additive[x]
  • deleted

See the Full Difference for further information

This analysis is available as XML or JSON.

See R3 <--> R4 Conversion Maps (status = 4 tests that all execute ok. All tests pass round-trip testing and 2 r3 resources are invalid (0 errors).)

 

Additional definitions: Master Definition XML + JSON, XML Schema/Schematron + JSON Schema, ShEx (for Turtle) + see the extensions, the spreadsheet version & the dependency analysis

PathDefinitionTypeReference
Specimen.status

Codes providing the status/availability of a specimen.

RequiredSpecimenStatus
Specimen.type

Concepts that describe the precise nature of an entity that may be used as the source material for an observation. This is one of two code systems that are used instead of table 0070 (code system xxxx) which conflated specimen types and specimen collection methods. Used in Version 2 messaging in the SPM segment.

ExampleHl7VSSpecimenType icon
Specimen.combined

Codes providing the combined status of a specimen.

RequiredSpecimenCombined
Specimen.role

Codes providing the role of a specimen.

PreferredSpecimenRole
Specimen.feature.type

This value set includes all codes from SNOMED CT icon where concept is-a 442083009 (Anatomical or acquired body site (body structure)).

ExampleSNOMEDCTBodyStructures
Specimen.collection.method

This example value set defines a set of codes that can be used to indicate the method by which a specimen was collected.

ExampleFHIRSpecimenCollectionMethod
Specimen.collection.device Example??
Specimen.collection.bodySite

This value set includes all codes from SNOMED CT icon where concept is-a 442083009 (Anatomical or acquired body site (body structure)).

ExampleSNOMEDCTBodyStructures
Specimen.collection.fastingStatus[x]

Value Set of codes that specify additional clinical information about the patient or specimen to report the supporting and/or suspected diagnosis and clinical findings on requests for interpreted diagnostic studies.

ExtensibleHl7VSRelevantClincialInformation icon
Specimen.processing.method

The technique that is used to perform the process or preserve the specimen.

ExampleSpecimenProcessingMethod
Specimen.condition

Concepts of modes or states of being that describe the nature of a specimen. Used in Version 2 messaging in the SPM segment.

ExtensibleHl7VSSpecimenCondition icon

Search parameters for this resource. The common parameters also apply. See Searching for more information about searching in REST, messaging, and services.

NameTypeDescriptionExpressionIn Common
accessiontokenThe accession number associated with the specimenSpecimen.accessionIdentifier
bodysitereferenceReference to a resource (by instance)Specimen.collection.bodySite.reference
collecteddateThe date the specimen was collectedSpecimen.collection.collected
collectorreferenceWho collected the specimenSpecimen.collection.collector
(Practitioner, Patient, PractitionerRole, RelatedPerson)
container-devicereferenceThe unique identifier associated with the specimen containerSpecimen.container.device.where(resolve() is Device)
(Device)
identifiertokenThe unique identifier associated with the specimenSpecimen.identifier
parentreferenceThe parent of the specimenSpecimen.parent
(Specimen)
patientreferenceThe patient the specimen comes fromSpecimen.subject.where(resolve() is Patient)
(Patient)
procedurereferenceThe procedure that collected the specimenSpecimen.collection.procedure
(Procedure)
status Ntokenavailable | unavailable | unsatisfactory | entered-in-errorSpecimen.status
subjectreferenceThe subject of the specimenSpecimen.subject
(Group, BiologicallyDerivedProduct, Device, Patient, Substance, Location)
typetokenThe specimen typeSpecimen.type