Release 4 R6 Ballot (1st Full Ballot)

This page is part of the FHIR Specification (v4.0.1: R4 - Mixed Normative and STU v6.0.0-ballot4: Release 6 Ballot (1st Full Ballot) (see Ballot Notes ) in it's permanent home (it will always be available at this URL). ). The current version which supercedes this version is 5.0.0 . For a full list of available versions, see the Directory of published versions for published versions icon . Page versions: R5 R4B R4 R3 R2

10.7 10.6 Resource Specimen - Content

Responsible Owner: Orders and Observations icon Work Group Maturity Level : 2   Trial Use Normative Security Category : Patient Compartments : Device , Group , Patient , Practitioner

A sample to be used for analysis.

10.7.1 10.6.1 Scope and Usage

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.

10.7.2 10.6.2 Background and Context

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.

This resource is referenced by

10.6.3 References to this Resource

10.7.3 10.6.4 Resource Content

Structure

External Identifier 0..* Material used in the Date and time of Period Σ 0..* Identifier Id for the container 0..1 Quantity 0..1 Additive associated with Reference
Name Flags Card. Type Description & Constraints      Filter: Filters doco
. . Specimen TU N DomainResource Sample for analysis
+ Rule: Specimen.collection.collector SHALL only be present if Specimen.collection.procedure is not present

Elements defined in Ancestors: id , meta , implicitRules , language , text , contained , extension , modifierExtension
. . . identifier Σ 0..* Identifier Primary specimen identifier
accessionIdentifier Σ 0..1 Identifier
Identifier assigned by the lab
. . . status ?! Σ 0..1 code available | unavailable | unsatisfactory | entered-in-error
SpecimenStatus Binding: Specimen Status ( Required )
. . . type Σ 0..1 CodeableConcept Kind of material that forms the specimen
Binding: hl7VS-specimenType icon v2 Specimen Type ( Example )
. . . receivedTime Σ 0..1 dateTime The time when specimen was is received for processing by the testing laboratory
. . . parent 0..* Reference ( Specimen ) Specimen from which this specimen originated

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

. . collection . combined Σ 0..1 code grouped | pooled
Binding: Specimen Combined ( Required )
... role 0..* CodeableConcept The role the specimen serves
Binding: Specimen Role ( Preferred )

... feature 0..* BackboneElement The physical feature of a specimen

. . . . type 1..1 CodeableConcept Highlighted feature
Binding: SNOMED CT Body Structures ( Example )
.... description 1..1 string Information about the feature
... collection 0..1 BackboneElement Collection details
. . . . collector Σ C 0..1 Reference ( Organization | Practitioner | PractitionerRole | Patient | RelatedPerson ) Who collected the specimen
. . . . collected[x] Σ 0..1 Collection time
. . . . . collectedDateTime dateTime
. . . . . collectedPeriod Period
. . . . duration Σ 0..1 Duration How long it took to collect specimen
. . . . quantity 0..1 SimpleQuantity The quantity of specimen collected
. . . . method 0..1 CodeableConcept Technique used to perform collection
Binding: FHIR Specimen Collection Method ( Example )
. . . bodySite . device[x] 0..1 Device used to perform collection
Binding: Specimen Container ( Example )
0..1
. . . . . deviceCodeableConcept CodeableConcept
. . . . . deviceReference Reference ( Device )
..... deviceCanonical canonical ( DeviceDefinition )
.... procedure C 0..1 Reference ( Procedure ) The procedure that collects the specimen
.... bodySite 0..1 CodeableReference ( BodyStructure ) Anatomical collection site
Binding: SNOMED CT Body Structures ( Example )
. . . . fastingStatus[x] Σ 0..1 Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation icon v2 Relevant Clincial Information ( Extensible )
. . . . . fastingStatusCodeableConcept CodeableConcept
. . . . . fastingStatusDuration Duration
. . . processing 0..* BackboneElement Processing and processing step details

. . . . description 0..1 string Textual description of procedure
. . . procedure . method 0..1 CodeableConcept Indicates the treatment step applied to the specimen
Binding: Specimen processing procedure Processing Method ( Example )
. . . additive . performer Σ 0..1 Reference ( Substance Practitioner | PractitionerRole | Patient | RelatedPerson ) Entity processing step specimen
. . . time[x] . device[x] 0..1 Device used to process the specimen processing
Binding: Processing Device Code ( Example )
. . . . timeDateTime . deviceCodeableConcept dateTime CodeableConcept
. . . timePeriod . . deviceReference Reference ( Device )
. . . . . deviceCanonical canonical ( DeviceDefinition )
. . . container . additive 0..* BackboneElement CodeableReference ( Substance | SubstanceDefinition ) Material used in the processing step
Direct container of specimen (tube/slide, etc.)
. . . identifier . time[x] 0..1 Date and time of specimen processing
. . . . . description timeDateTime 0..1 string dateTime Textual description of the container
. . . . . type timePeriod 0..1 CodeableConcept Period Kind of container directly associated with specimen Specimen container ( Example )
. . . capacity . . timeDuration 0..1 SimpleQuantity Duration Container volume or size
. . specimenQuantity . container 0..* SimpleQuantity BackboneElement Direct container of specimen within container (tube/slide, etc.)

. . . . additive[x] device[x] 1..1 Device resource for the container
v2 Additive Binding: Container Device Code ( Example )
. . . . . additiveCodeableConcept deviceCodeableConcept CodeableConcept
. . . . . additiveReference deviceReference Reference ( Device )
. . . . . deviceCanonical canonical ( Substance DeviceDefinition )
. . . . specimenQuantity 0..1 SimpleQuantity Quantity of specimen within container
. . . condition Σ 0..* CodeableConcept State of the specimen
Binding: hl7VS-specimenCondition icon v2 Specimen Condition ( Extensible Example )

. . . note 0..* Annotation Comments


doco Documentation for this format icon

See the Extensions for this resource

UML Diagram ( Legend )

Specimen ( DomainResource ) Id Identifiers used for specimen identifier : Identifier [0..*] The identifier assigned by the lab when accessioning specimen(s). This is identification. These could include but are not necessarily the same as the limited to identifiers generated upon collection, accessioning, or other reasons for labeling a specimen identifier, depending on local lab procedures accessionIdentifier identifier : Identifier [0..1] [0..*] The availability of the specimen (this element modifies the meaning of other elements) status : code [0..1] « Codes providing the status/availability of a specimen. null (Strength=Required) SpecimenStatus ! » The kind of material that forms the specimen type : CodeableConcept [0..1] « The type of the specimen. null (Strength=Example) v2.0487 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 substance, a biologically-derived product, or a device subject : Reference [0..1] « Patient | Group | Device | BiologicallyDerivedProduct | Substance | Location | NutritionProduct » Time when specimen was is received by the testing laboratory for processing or testing receivedTime : dateTime [0..1] Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimen parent : Reference [0..*] « Specimen » Details concerning a service request that required a specimen to be collected request : Reference [0..*] « ServiceRequest » This element signifies if the specimen is part of a group or pooled combined : code [0..1] « null (Strength=Required) SpecimenCombined ! » The role or reason for the specimen in the testing workflow role : CodeableConcept [0..*] « Codes describing specimen role. (Strength=Preferred) SpecimenRole ? » A mode or state of being that describes the nature of the specimen condition : CodeableConcept [0..*] « Codes describing the state of the specimen. (Strength=Extensible) null (Strength=Example) v2.0493 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..*] Feature The landmark or feature being highlighted type : CodeableConcept [1..1] « Codes describing anatomical feature. (Strength=Example) SNOMEDCTBodyStructures ?? » Description of the feature of the specimen description : string [1..1] Collection Person who collected the specimen collector : Reference [0..1] « Organization | Practitioner | PractitionerRole | Patient | RelatedPerson » « This element has or is affected by some invariants C » Time when specimen was collected from subject - the physiologically relevant time collected[x] : Type DataType [0..1] « dateTime | Period » The span of time over which the collection of a specimen occurred duration : Duration [0..1] The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample quantity : Quantity ( SimpleQuantity ) [0..1] A coded value specifying the technique that is used to perform the procedure method : CodeableConcept [0..1] « The technique null (Strength=Example) FHIRSpecimenCollectionMethod ?? » A coded value specifying the device that is used to perform the procedure. procedure device[x] : DataType [0..1] « CodeableConcept | Reference ( Device )| canonical ( DeviceDefinition ); null (Strength=Example) FHIRSpecimenCollectionMethod SpecimenContainer ?? » 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 » « This element has or is affected by some invariants C » 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 specimens bodySite : CodeableConcept CodeableReference [0..1] « BodyStructure ; Codes describing anatomical locations. May include laterality. (Strength=Example) SNOMEDCTBodyStructures ?? » Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection fastingStatus[x] : Type DataType [0..1] « CodeableConcept | Duration ; Codes describing the fasting status of the patient. null (Strength=Extensible) v2.0916 Hl7VSRelevantClincialInformat... + » Processing Textual description of procedure description : string [0..1] A coded value specifying the procedure method used to process the specimen procedure method : CodeableConcept [0..1] « Type indicating null (Strength=Example) SpecimenProcessingMethod ?? » The performer of the technique processing of the specimen performer : Reference [0..1] « Practitioner | PractitionerRole | Patient | RelatedPerson » The device used to process in the specimen. processing of the specimen device[x] : DataType [0..1] « CodeableConcept | Reference ( Device )| canonical ( DeviceDefinition ); null (Strength=Example) SpecimenProcessingProcedure ProcessingDeviceCode ?? » Material used in the processing step additive : Reference CodeableReference [0..*] « Substance | SubstanceDefinition » 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 formalin time[x] : Type DataType [0..1] « dateTime | Period | Duration » Container Id for container. There may be multiple; a manufacturer's bar code, lab assigned identifier, etc. The device resource for the the container ID may differ from holding the specimen id specimen. If the container is in some circumstances a holder then the referenced device will point to a parent device identifier device[x] : Identifier DataType [0..*] Textual description of the container description [1..1] « CodeableConcept : string | Reference [0..1] ( Device )| The type of container associated with the specimen (e.g. slide, aliquot, etc.) type canonical : CodeableConcept ( DeviceDefinition [0..1] « ); Type of specimen container. null (Strength=Example) SpecimenContainer ContainerDeviceCode ?? » The capacity (volume or other measure) the container may contain capacity : Quantity ( SimpleQuantity ) [0..1] The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type specimenQuantity : Quantity ( SimpleQuantity ) [0..1] Introduced substance to preserve, maintain A physical feature or enhance landmark on a specimen, highlighted for context by the collector of the specimen. Examples: Formalin, Citrate, EDTA additive[x] : Type [0..1] « CodeableConcept | Reference ( Substance ); Substance added to specimen container. (Strength=Example) (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 v2.0371 ?? » [0..*] Details concerning the specimen collection collection [0..1] Details concerning processing and processing steps for the specimen processing [0..*] The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here container [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>
 <</accessionIdentifier>

 <identifier><!-- 0..* Identifier Primary specimen identifier --></identifier>

 <status value="[code]"/><!-- 0..1 available | unavailable | unsatisfactory | entered-in-error -->
 <</type>
 <</subject>
 <

 <type><!-- 0..1 CodeableConcept Kind of material that forms the specimen icon --></type>
 <subject><!-- 0..1 Reference(BiologicallyDerivedProduct|Device|Group|Location|
   NutritionProduct|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>

  <collector><!-- I 0..1 Reference(Organization|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>
  <</bodySite>
  <</fastingStatus[x]>

  <device[x]><!-- 0..1 CodeableConcept|Reference(Device)|canonical(
    DeviceDefinition) Device used to perform collection --></device[x]>

  <procedure><!-- I 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 -->
  <</procedure>
  <</additive>
  <</time[x]>

  <method><!-- 0..1 CodeableConcept Indicates the treatment step  applied to the specimen --></method>
  <performer><!-- 0..1 Reference(Patient|Practitioner|PractitionerRole|
    RelatedPerson) Entity processing specimen --></performer>

  <device[x]><!-- 0..1 CodeableConcept|Reference(Device)|canonical(
    DeviceDefinition) Device used to process the specimen --></device[x]>

  <additive><!-- 0..* CodeableReference(Substance|SubstanceDefinition) Material used in the processing step --></additive>
  <time[x]><!-- 0..1 dateTime|Period|Duration Date and time of specimen processing --></time[x]>

 </processing>
 <container>  <!-- 0..* Direct container of specimen (tube/slide, etc.) -->
  <</identifier>
  <
  <</type>
  <</capacity>

  <device[x]><!-- 1..1 CodeableConcept|Reference(Device)|canonical(
    DeviceDefinition) Device resource for the container --></device[x]>
  <specimenQuantity><!-- 0..1 Quantity(SimpleQuantity) Quantity of specimen within container --></specimenQuantity>
  <</additive[x]>

 </container>
 <</condition>

 <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 }], // Primary specimen identifier

  "status" : "<code>", // available | unavailable | unsatisfactory | entered-in-error
  "
  "
  "

  "type" : { CodeableConcept }, // Kind of material that forms the specimen icon
  "subject" : { Reference(BiologicallyDerivedProduct|Device|Group|Location|
   NutritionProduct|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(Organization|Patient|Practitioner|
    PractitionerRole|RelatedPerson) }, // I 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[x]: Device used to perform collection. One of these 3:
    "deviceCodeableConcept" : { CodeableConcept },
    "deviceReference" : { Reference(Device) },
    "deviceCanonical" : "<canonical(DeviceDefinition)>",
    "procedure" : { Reference(Procedure) }, // I 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
    "performer" : { Reference(Patient|Practitioner|PractitionerRole|
    RelatedPerson) }, // Entity processing specimen
    // device[x]: Device used to process the specimen. One of these 3:

    "deviceCodeableConcept" : { CodeableConcept },
    "deviceReference" : { Reference(Device) },
    "deviceCanonical" : "<canonical(DeviceDefinition)>",
    "additive" : [{ CodeableReference(Substance|SubstanceDefinition) }], // Material used in the processing step
    // time[x]: Date and time of specimen processing. One of these 3:

    "timeDateTime" : "<dateTime>",
    "timePeriod" : { Period },
    "timeDuration" : { Duration }

  }],
  "container" : [{ // Direct container of specimen (tube/slide, etc.)
    "
    "
    "
    "
    "
    
    " }
    " }

    // device[x]: Device resource for the container. One of these 3:
    "deviceCodeableConcept" : { CodeableConcept },
    "deviceReference" : { Reference(Device) },
    "deviceCanonical" : "<canonical(DeviceDefinition)>",
    "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 
  # from 
  fhir:
  fhir:
  fhir:
  fhir:
  fhir:
  fhir:
  fhir:
  fhir:
  fhir:
    fhir:
    # . One of these 2
      fhir: ]
      fhir: ]
    fhir:
    fhir:
    fhir:
    fhir:
    # . One of these 2
      fhir: ]
      fhir: ]
  ];
  fhir:
    fhir:
    fhir:
    fhir:
    # . One of these 2
      fhir: ]
      fhir: ]
  ], ...;
  fhir:
    fhir:
    fhir:
    fhir:
    fhir:
    fhir:
    # . One of these 2
      fhir: ]
      fhir:) ]
  ], ...;
  fhir:
  fhir:

  # from Resource: fhir:id, fhir:meta, fhir:implicitRules, and fhir:language
  # from DomainResource: fhir:text, fhir:contained, fhir:extension, and fhir:modifierExtension
  fhir:identifier  ( [ Identifier ] ... ) ; # 0..* Primary specimen identifier
  fhir:status [ code ] ; # 0..1 available | unavailable | unsatisfactory | entered-in-error
  fhir:type [ CodeableConcept ] ; # 0..1 Kind of material that forms the specimen
  fhir:subject [ Reference(BiologicallyDerivedProduct|Device|Group|Location|NutritionProduct|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:receivedTime [ dateTime ] ; # 0..1 The time when specimen is received by the testing laboratory
  fhir:parent  ( [ Reference(Specimen) ] ... ) ; # 0..* Specimen from which this specimen originated
  fhir:request  ( [ Reference(ServiceRequest) ] ... ) ; # 0..* Why the specimen was collected
  fhir:combined [ code ] ; # 0..1 grouped | pooled
  fhir:role  ( [ CodeableConcept ] ... ) ; # 0..* The role the specimen serves
  fhir:feature ( [ # 0..* The physical feature of a specimen
    fhir:type [ CodeableConcept ] ; # 1..1 Highlighted feature
    fhir:description [ string ] ; # 1..1 Information about the feature
  ] ... ) ;
  fhir:collection [ # 0..1 Collection details
    fhir:collector [ Reference(Organization|Patient|Practitioner|PractitionerRole|RelatedPerson) ] ; # 0..1 I Who collected the specimen
    # collected[x] : 0..1 Collection time. One of these 2
      fhir:collected [  a fhir:DateTime ; dateTime ]
      fhir:collected [  a fhir:Period ; Period ]
    fhir:duration [ Duration ] ; # 0..1 How long it took to collect specimen
    fhir:quantity [ Quantity(SimpleQuantity) ] ; # 0..1 The quantity of specimen collected
    fhir:method [ CodeableConcept ] ; # 0..1 Technique used to perform collection
    # device[x] : 0..1 Device used to perform collection. One of these 3
      fhir:device [  a fhir:CodeableConcept ; CodeableConcept ]
      fhir:device [  a fhir:Reference ; Reference(Device) ]
      fhir:device [  a fhir:Canonical ; canonical(DeviceDefinition) ]
    fhir:procedure [ Reference(Procedure) ] ; # 0..1 I The procedure that collects the specimen
    fhir:bodySite [ CodeableReference(BodyStructure) ] ; # 0..1 Anatomical collection site
    # fastingStatus[x] : 0..1 Whether or how long patient abstained from food and/or drink. One of these 2
      fhir:fastingStatus [  a fhir:CodeableConcept ; CodeableConcept ]
      fhir:fastingStatus [  a fhir:Duration ; Duration ]
  ] ;
  fhir:processing ( [ # 0..* Processing and processing step details
    fhir:description [ string ] ; # 0..1 Textual description of procedure
    fhir:method [ CodeableConcept ] ; # 0..1 Indicates the treatment step  applied to the specimen
    fhir:performer [ Reference(Patient|Practitioner|PractitionerRole|RelatedPerson) ] ; # 0..1 Entity processing specimen
    # device[x] : 0..1 Device used to process the specimen. One of these 3
      fhir:device [  a fhir:CodeableConcept ; CodeableConcept ]
      fhir:device [  a fhir:Reference ; Reference(Device) ]
      fhir:device [  a fhir:Canonical ; canonical(DeviceDefinition) ]
    fhir:additive  ( [ CodeableReference(Substance|SubstanceDefinition) ] ... ) ; # 0..* Material used in the processing step
    # time[x] : 0..1 Date and time of specimen processing. One of these 3
      fhir:time [  a fhir:DateTime ; dateTime ]
      fhir:time [  a fhir:Period ; Period ]
      fhir:time [  a fhir:Duration ; Duration ]
  ] ... ) ;
  fhir:container ( [ # 0..* Direct container of specimen (tube/slide, etc.)
    # device[x] : 1..1 Device resource for the container. One of these 3
      fhir:device [  a fhir:CodeableConcept ; CodeableConcept ]
      fhir:device [  a fhir:Reference ; Reference(Device) ]
      fhir:device [  a fhir:Canonical ; canonical(DeviceDefinition) ]
    fhir:specimenQuantity [ Quantity(SimpleQuantity) ] ; # 0..1 Quantity of specimen within container
  ] ... ) ;
  fhir:condition  ( [ CodeableConcept ] ... ) ; # 0..* State of the specimen
  fhir:note  ( [ Annotation ] ... ) ; # 0..* Comments

]

Changes since R3 from R5 to R6

Specimen
Specimen.status Specimen.subject
  • Change value set Type Reference: Added Target Type NutritionProduct
Specimen.collection.collector
  • Type Reference: Added Target Type Organization
Specimen.collection.device[x]
  • Renamed from http://hl7.org/fhir/ValueSet/specimen-status device to http://hl7.org/fhir/ValueSet/specimen-status|4.0.1 device[x]
  • Add Types CodeableConcept, Reference(Device), canonical(DeviceDefinition)
  • Remove Type CodeableReference
Specimen.processing.performer
  • Added Element
Specimen.processing.device[x]
  • Added Element
Specimen.subject Specimen.processing.additive
  • Min Cardinality Type changed from 1 Reference(Substance) to 0 CodeableReference
Specimen.processing.time[x]
  • Add Type Reference: Added Target Type Location Duration
Specimen.container.device[x]
  • Renamed from device to device[x]
  • Add Types CodeableConcept, canonical(DeviceDefinition)
Specimen.request Specimen.condition
  • Remove Binding `http://terminology.hl7.org/ValueSet/v2-0493` (extensible)
Specimen.accessionIdentifier
  • Deleted (-> Specimen.identifier (along with all the other identifiers))
Specimen.container.location
  • Deleted

Changes from R4 and R4B to R6

Specimen
Specimen.subject
  • Type Reference: Added Target Type ServiceRequest Types BiologicallyDerivedProduct, NutritionProduct
Specimen.combined
  • Added Element
Specimen.role
  • Type Reference: Removed Target Type ProcedureRequest 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 Organization, Patient, RelatedPerson
Specimen.collection.device[x]
  • Added Element
Specimen.collection.procedure
  • Added Element
Specimen.collection.bodySite
  • Type PractitionerRole changed from CodeableConcept to CodeableReference
Specimen.processing.method
  • Renamed from procedure to method
Specimen.collection.duration Specimen.processing.performer
  • Added Element
Specimen.collection.fastingStatus[x] Specimen.processing.device[x]
  • Added Element
Specimen.processing.additive
  • Type changed from Reference(Substance) to CodeableReference
Specimen.processing.time[x]
  • Add Type Duration
Specimen.condition Specimen.container.device[x]
  • Added Mandatory Element
Specimen.condition
  • Remove Binding `http://terminology.hl7.org/ValueSet/v2-0493` (extensible)
Specimen.accessionIdentifier
  • Deleted (-> Specimen.identifier (along with all the other identifiers))
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 for R4 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). ) for R4B as XML or JSON .

Structure

External Identifier 0..* Material used in the Date and time of Period Σ 0..* Identifier Id for the container 0..1 Quantity 0..1 Additive associated with Reference
Name Flags Card. Type Description & Constraints      Filter: Filters doco
. . Specimen TU N DomainResource Sample for analysis
+ Rule: Specimen.collection.collector SHALL only be present if Specimen.collection.procedure is not present

Elements defined in Ancestors: id , meta , implicitRules , language , text , contained , extension , modifierExtension
. . . identifier Σ 0..* Identifier Primary specimen identifier
accessionIdentifier Σ 0..1 Identifier
Identifier assigned by the lab
. . . status ?! Σ 0..1 code available | unavailable | unsatisfactory | entered-in-error
SpecimenStatus Binding: Specimen Status ( Required )
. . . type Σ 0..1 CodeableConcept Kind of material that forms the specimen
Binding: hl7VS-specimenType icon v2 Specimen Type ( Example )
. . . receivedTime Σ 0..1 dateTime The time when specimen was is received for processing by the testing laboratory
. . . parent 0..* Reference ( Specimen ) Specimen from which this specimen originated

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

. . collection . combined Σ 0..1 code grouped | pooled
Binding: Specimen Combined ( Required )
... role 0..* CodeableConcept The role the specimen serves
Binding: Specimen Role ( Preferred )

... feature 0..* BackboneElement The physical feature of a specimen

.... type 1..1 CodeableConcept Highlighted feature
Binding: SNOMED CT Body Structures ( Example )
.... description 1..1 string Information about the feature
... collection 0..1 BackboneElement Collection details
. . . . collector Σ C 0..1 Reference ( Organization | Practitioner | PractitionerRole | Patient | RelatedPerson ) Who collected the specimen
. . . . collected[x] Σ 0..1 Collection time
. . . . . collectedDateTime dateTime
. . . . . collectedPeriod Period
. . . . duration Σ 0..1 Duration How long it took to collect specimen
. . . . quantity 0..1 SimpleQuantity The quantity of specimen collected
. . . . method 0..1 CodeableConcept Technique used to perform collection
Binding: FHIR Specimen Collection Method ( Example )
. . . bodySite . device[x] 0..1 Device used to perform collection
Binding: Specimen Container ( Example )
0..1
. . . . . deviceCodeableConcept CodeableConcept
. . . . . deviceReference Reference ( Device )
..... deviceCanonical canonical ( DeviceDefinition )
.... procedure C 0..1 Reference ( Procedure ) The procedure that collects the specimen
.... bodySite 0..1 CodeableReference ( BodyStructure ) Anatomical collection site
Binding: SNOMED CT Body Structures ( Example )
. . . . fastingStatus[x] Σ 0..1 Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation icon v2 Relevant Clincial Information ( Extensible )
. . . . . fastingStatusCodeableConcept CodeableConcept
. . . . . fastingStatusDuration Duration
. . . processing 0..* BackboneElement Processing and processing step details

. . . . description 0..1 string Textual description of procedure
. . . procedure . method 0..1 CodeableConcept Indicates the treatment step applied to the specimen
Binding: Specimen processing procedure Processing Method ( Example )
. . . additive . performer Σ 0..1 Reference ( Substance Practitioner | PractitionerRole | Patient | RelatedPerson ) Entity processing step specimen
. . . time[x] . device[x] 0..1 Device used to process the specimen processing
Binding: Processing Device Code ( Example )
. . . . timeDateTime . deviceCodeableConcept dateTime CodeableConcept
. . . timePeriod . . deviceReference Reference ( Device )
. . . . . deviceCanonical canonical ( DeviceDefinition )
. . . container . additive 0..* BackboneElement CodeableReference ( Substance | SubstanceDefinition ) Material used in the processing step
Direct container of specimen (tube/slide, etc.)
. . . identifier . time[x] 0..1 Date and time of specimen processing
. . . . . description timeDateTime 0..1 string dateTime Textual description of the container
. . . . . type timePeriod 0..1 CodeableConcept Period Kind of container directly associated with specimen Specimen container ( Example )
. . . capacity . . timeDuration 0..1 SimpleQuantity Duration Container volume or size
. . specimenQuantity . container 0..* SimpleQuantity BackboneElement Direct container of specimen within container (tube/slide, etc.)

. . . . additive[x] device[x] 1..1 Device resource for the container
v2 Additive Binding: Container Device Code ( Example )
. . . . . additiveCodeableConcept deviceCodeableConcept CodeableConcept
. . . . . additiveReference deviceReference Reference ( Device )
. . . . . deviceCanonical canonical ( Substance DeviceDefinition )
. . . . specimenQuantity 0..1 SimpleQuantity Quantity of specimen within container
. . . condition Σ 0..* CodeableConcept State of the specimen
Binding: hl7VS-specimenCondition icon v2 Specimen Condition ( Extensible Example )

. . . note 0..* Annotation Comments


doco Documentation for this format icon

See the Extensions for this resource

UML Diagram ( Legend )

Specimen ( DomainResource ) Id Identifiers used for specimen identifier : Identifier [0..*] The identifier assigned by the lab when accessioning specimen(s). This is identification. These could include but are not necessarily the same as the limited to identifiers generated upon collection, accessioning, or other reasons for labeling a specimen identifier, depending on local lab procedures accessionIdentifier identifier : Identifier [0..1] [0..*] The availability of the specimen (this element modifies the meaning of other elements) status : code [0..1] « Codes providing the status/availability of a specimen. null (Strength=Required) SpecimenStatus ! » The kind of material that forms the specimen type : CodeableConcept [0..1] « The type of the specimen. null (Strength=Example) v2.0487 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 substance, a biologically-derived product, or a device subject : Reference [0..1] « Patient | Group | Device | BiologicallyDerivedProduct | Substance | Location | NutritionProduct » Time when specimen was is received by the testing laboratory for processing or testing receivedTime : dateTime [0..1] Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimen parent : Reference [0..*] « Specimen » Details concerning a service request that required a specimen to be collected request : Reference [0..*] « ServiceRequest » This element signifies if the specimen is part of a group or pooled combined : code [0..1] « null (Strength=Required) SpecimenCombined ! » The role or reason for the specimen in the testing workflow role : CodeableConcept [0..*] « Codes describing specimen role. (Strength=Preferred) SpecimenRole ? » A mode or state of being that describes the nature of the specimen condition : CodeableConcept [0..*] « Codes describing the state of the specimen. (Strength=Extensible) null (Strength=Example) v2.0493 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..*] Feature The landmark or feature being highlighted type : CodeableConcept [1..1] « Codes describing anatomical feature. (Strength=Example) SNOMEDCTBodyStructures ?? » Description of the feature of the specimen description : string [1..1] Collection Person who collected the specimen collector : Reference [0..1] « Organization | Practitioner | PractitionerRole | Patient | RelatedPerson » « This element has or is affected by some invariants C » Time when specimen was collected from subject - the physiologically relevant time collected[x] : Type DataType [0..1] « dateTime | Period » The span of time over which the collection of a specimen occurred duration : Duration [0..1] The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample quantity : Quantity ( SimpleQuantity ) [0..1] A coded value specifying the technique that is used to perform the procedure method : CodeableConcept [0..1] « The technique null (Strength=Example) FHIRSpecimenCollectionMethod ?? » A coded value specifying the device that is used to perform the procedure. procedure device[x] : DataType [0..1] « CodeableConcept | Reference ( Device )| canonical ( DeviceDefinition ); null (Strength=Example) FHIRSpecimenCollectionMethod SpecimenContainer ?? » 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 » « This element has or is affected by some invariants C » 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 specimens bodySite : CodeableConcept CodeableReference [0..1] « BodyStructure ; Codes describing anatomical locations. May include laterality. (Strength=Example) SNOMEDCTBodyStructures ?? » Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection fastingStatus[x] : Type DataType [0..1] « CodeableConcept | Duration ; Codes describing the fasting status of the patient. null (Strength=Extensible) v2.0916 Hl7VSRelevantClincialInformat... + » Processing Textual description of procedure description : string [0..1] A coded value specifying the procedure method used to process the specimen procedure method : CodeableConcept [0..1] « Type indicating null (Strength=Example) SpecimenProcessingMethod ?? » The performer of the technique processing of the specimen performer : Reference [0..1] « Practitioner | PractitionerRole | Patient | RelatedPerson » The device used to process in the specimen. processing of the specimen device[x] : DataType [0..1] « CodeableConcept | Reference ( Device )| canonical ( DeviceDefinition ); null (Strength=Example) SpecimenProcessingProcedure ProcessingDeviceCode ?? » Material used in the processing step additive : Reference CodeableReference [0..*] « Substance | SubstanceDefinition » 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 formalin time[x] : Type DataType [0..1] « dateTime | Period | Duration » Container Id for container. There may be multiple; a manufacturer's bar code, lab assigned identifier, etc. The device resource for the the container ID may differ from holding the specimen id specimen. If the container is in some circumstances a holder then the referenced device will point to a parent device identifier device[x] : Identifier DataType [0..*] Textual description of the container description [1..1] « CodeableConcept : string | Reference [0..1] ( Device )| The type of container associated with the specimen (e.g. slide, aliquot, etc.) type canonical : CodeableConcept ( DeviceDefinition [0..1] « ); Type of specimen container. null (Strength=Example) SpecimenContainer ContainerDeviceCode ?? » The capacity (volume or other measure) the container may contain capacity : Quantity ( SimpleQuantity ) [0..1] The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type specimenQuantity : Quantity ( SimpleQuantity ) [0..1] Introduced substance to preserve, maintain A physical feature or enhance landmark on a specimen, highlighted for context by the collector of the specimen. Examples: Formalin, Citrate, EDTA additive[x] : Type [0..1] « CodeableConcept | Reference ( Substance ); Substance added to specimen container. (Strength=Example) (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 v2.0371 ?? » [0..*] Details concerning the specimen collection collection [0..1] Details concerning processing and processing steps for the specimen processing [0..*] The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here container [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>
 <</accessionIdentifier>

 <identifier><!-- 0..* Identifier Primary specimen identifier --></identifier>

 <status value="[code]"/><!-- 0..1 available | unavailable | unsatisfactory | entered-in-error -->
 <</type>
 <</subject>
 <

 <type><!-- 0..1 CodeableConcept Kind of material that forms the specimen icon --></type>
 <subject><!-- 0..1 Reference(BiologicallyDerivedProduct|Device|Group|Location|
   NutritionProduct|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>

  <collector><!-- I 0..1 Reference(Organization|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>
  <</bodySite>
  <</fastingStatus[x]>

  <device[x]><!-- 0..1 CodeableConcept|Reference(Device)|canonical(
    DeviceDefinition) Device used to perform collection --></device[x]>

  <procedure><!-- I 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 -->
  <</procedure>
  <</additive>
  <</time[x]>

  <method><!-- 0..1 CodeableConcept Indicates the treatment step  applied to the specimen --></method>
  <performer><!-- 0..1 Reference(Patient|Practitioner|PractitionerRole|
    RelatedPerson) Entity processing specimen --></performer>

  <device[x]><!-- 0..1 CodeableConcept|Reference(Device)|canonical(
    DeviceDefinition) Device used to process the specimen --></device[x]>

  <additive><!-- 0..* CodeableReference(Substance|SubstanceDefinition) Material used in the processing step --></additive>
  <time[x]><!-- 0..1 dateTime|Period|Duration Date and time of specimen processing --></time[x]>

 </processing>
 <container>  <!-- 0..* Direct container of specimen (tube/slide, etc.) -->
  <</identifier>
  <
  <</type>
  <</capacity>

  <device[x]><!-- 1..1 CodeableConcept|Reference(Device)|canonical(
    DeviceDefinition) Device resource for the container --></device[x]>
  <specimenQuantity><!-- 0..1 Quantity(SimpleQuantity) Quantity of specimen within container --></specimenQuantity>
  <</additive[x]>

 </container>
 <</condition>

 <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 }], // Primary specimen identifier

  "status" : "<code>", // available | unavailable | unsatisfactory | entered-in-error
  "
  "
  "

  "type" : { CodeableConcept }, // Kind of material that forms the specimen icon
  "subject" : { Reference(BiologicallyDerivedProduct|Device|Group|Location|
   NutritionProduct|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(Organization|Patient|Practitioner|
    PractitionerRole|RelatedPerson) }, // I 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[x]: Device used to perform collection. One of these 3:
    "deviceCodeableConcept" : { CodeableConcept },
    "deviceReference" : { Reference(Device) },
    "deviceCanonical" : "<canonical(DeviceDefinition)>",
    "procedure" : { Reference(Procedure) }, // I 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
    "performer" : { Reference(Patient|Practitioner|PractitionerRole|
    RelatedPerson) }, // Entity processing specimen
    // device[x]: Device used to process the specimen. One of these 3:

    "deviceCodeableConcept" : { CodeableConcept },
    "deviceReference" : { Reference(Device) },
    "deviceCanonical" : "<canonical(DeviceDefinition)>",
    "additive" : [{ CodeableReference(Substance|SubstanceDefinition) }], // Material used in the processing step
    // time[x]: Date and time of specimen processing. One of these 3:

    "timeDateTime" : "<dateTime>",
    "timePeriod" : { Period },
    "timeDuration" : { Duration }

  }],
  "container" : [{ // Direct container of specimen (tube/slide, etc.)
    "
    "
    "
    "
    "
    
    " }
    " }

    // device[x]: Device resource for the container. One of these 3:
    "deviceCodeableConcept" : { CodeableConcept },
    "deviceReference" : { Reference(Device) },
    "deviceCanonical" : "<canonical(DeviceDefinition)>",
    "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 
  # from 
  fhir:
  fhir:
  fhir:
  fhir:
  fhir:
  fhir:
  fhir:
  fhir:
  fhir:
    fhir:
    # . One of these 2
      fhir: ]
      fhir: ]
    fhir:
    fhir:
    fhir:
    fhir:
    # . One of these 2
      fhir: ]
      fhir: ]
  ];
  fhir:
    fhir:
    fhir:
    fhir:
    # . One of these 2
      fhir: ]
      fhir: ]
  ], ...;
  fhir:
    fhir:
    fhir:
    fhir:
    fhir:
    fhir:
    # . One of these 2
      fhir: ]
      fhir:) ]
  ], ...;
  fhir:
  fhir:

  # from Resource: fhir:id, fhir:meta, fhir:implicitRules, and fhir:language
  # from DomainResource: fhir:text, fhir:contained, fhir:extension, and fhir:modifierExtension
  fhir:identifier  ( [ Identifier ] ... ) ; # 0..* Primary specimen identifier
  fhir:status [ code ] ; # 0..1 available | unavailable | unsatisfactory | entered-in-error
  fhir:type [ CodeableConcept ] ; # 0..1 Kind of material that forms the specimen
  fhir:subject [ Reference(BiologicallyDerivedProduct|Device|Group|Location|NutritionProduct|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:receivedTime [ dateTime ] ; # 0..1 The time when specimen is received by the testing laboratory
  fhir:parent  ( [ Reference(Specimen) ] ... ) ; # 0..* Specimen from which this specimen originated
  fhir:request  ( [ Reference(ServiceRequest) ] ... ) ; # 0..* Why the specimen was collected
  fhir:combined [ code ] ; # 0..1 grouped | pooled
  fhir:role  ( [ CodeableConcept ] ... ) ; # 0..* The role the specimen serves
  fhir:feature ( [ # 0..* The physical feature of a specimen
    fhir:type [ CodeableConcept ] ; # 1..1 Highlighted feature
    fhir:description [ string ] ; # 1..1 Information about the feature
  ] ... ) ;
  fhir:collection [ # 0..1 Collection details
    fhir:collector [ Reference(Organization|Patient|Practitioner|PractitionerRole|RelatedPerson) ] ; # 0..1 I Who collected the specimen
    # collected[x] : 0..1 Collection time. One of these 2
      fhir:collected [  a fhir:DateTime ; dateTime ]
      fhir:collected [  a fhir:Period ; Period ]
    fhir:duration [ Duration ] ; # 0..1 How long it took to collect specimen
    fhir:quantity [ Quantity(SimpleQuantity) ] ; # 0..1 The quantity of specimen collected
    fhir:method [ CodeableConcept ] ; # 0..1 Technique used to perform collection
    # device[x] : 0..1 Device used to perform collection. One of these 3
      fhir:device [  a fhir:CodeableConcept ; CodeableConcept ]
      fhir:device [  a fhir:Reference ; Reference(Device) ]
      fhir:device [  a fhir:Canonical ; canonical(DeviceDefinition) ]
    fhir:procedure [ Reference(Procedure) ] ; # 0..1 I The procedure that collects the specimen
    fhir:bodySite [ CodeableReference(BodyStructure) ] ; # 0..1 Anatomical collection site
    # fastingStatus[x] : 0..1 Whether or how long patient abstained from food and/or drink. One of these 2
      fhir:fastingStatus [  a fhir:CodeableConcept ; CodeableConcept ]
      fhir:fastingStatus [  a fhir:Duration ; Duration ]
  ] ;
  fhir:processing ( [ # 0..* Processing and processing step details
    fhir:description [ string ] ; # 0..1 Textual description of procedure
    fhir:method [ CodeableConcept ] ; # 0..1 Indicates the treatment step  applied to the specimen
    fhir:performer [ Reference(Patient|Practitioner|PractitionerRole|RelatedPerson) ] ; # 0..1 Entity processing specimen
    # device[x] : 0..1 Device used to process the specimen. One of these 3
      fhir:device [  a fhir:CodeableConcept ; CodeableConcept ]
      fhir:device [  a fhir:Reference ; Reference(Device) ]
      fhir:device [  a fhir:Canonical ; canonical(DeviceDefinition) ]
    fhir:additive  ( [ CodeableReference(Substance|SubstanceDefinition) ] ... ) ; # 0..* Material used in the processing step
    # time[x] : 0..1 Date and time of specimen processing. One of these 3
      fhir:time [  a fhir:DateTime ; dateTime ]
      fhir:time [  a fhir:Period ; Period ]
      fhir:time [  a fhir:Duration ; Duration ]
  ] ... ) ;
  fhir:container ( [ # 0..* Direct container of specimen (tube/slide, etc.)
    # device[x] : 1..1 Device resource for the container. One of these 3
      fhir:device [  a fhir:CodeableConcept ; CodeableConcept ]
      fhir:device [  a fhir:Reference ; Reference(Device) ]
      fhir:device [  a fhir:Canonical ; canonical(DeviceDefinition) ]
    fhir:specimenQuantity [ Quantity(SimpleQuantity) ] ; # 0..1 Quantity of specimen within container
  ] ... ) ;
  fhir:condition  ( [ CodeableConcept ] ... ) ; # 0..* State of the specimen
  fhir:note  ( [ Annotation ] ... ) ; # 0..* Comments

]

Changes since Release 3 from R5 to R6

Specimen
Specimen.status Specimen.subject
  • Change value set Type Reference: Added Target Type NutritionProduct
Specimen.collection.collector
  • Type Reference: Added Target Type Organization
Specimen.collection.device[x]
  • Renamed from http://hl7.org/fhir/ValueSet/specimen-status device to http://hl7.org/fhir/ValueSet/specimen-status|4.0.1 device[x]
  • Add Types CodeableConcept, Reference(Device), canonical(DeviceDefinition)
  • Remove Type CodeableReference
Specimen.processing.performer
  • Added Element
Specimen.processing.device[x]
  • Added Element
Specimen.subject Specimen.processing.additive
  • Min Cardinality Type changed from 1 Reference(Substance) to 0 CodeableReference
Specimen.processing.time[x]
  • Add Type Reference: Added Target Type Location Duration
Specimen.container.device[x]
  • Renamed from device to device[x]
  • Add Types CodeableConcept, canonical(DeviceDefinition)
Specimen.request Specimen.condition
  • Remove Binding `http://terminology.hl7.org/ValueSet/v2-0493` (extensible)
Specimen.accessionIdentifier
  • Deleted (-> Specimen.identifier (along with all the other identifiers))
Specimen.container.location
  • Deleted

Changes from R4 and R4B to R6

Specimen
Specimen.subject
  • Type Reference: Added Target Type ServiceRequest Types BiologicallyDerivedProduct, NutritionProduct
Specimen.combined
  • Type Reference: Removed Target Type ProcedureRequest 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 Organization, Patient, RelatedPerson
Specimen.collection.device[x]
  • Added Element
Specimen.collection.procedure
  • Added Element
Specimen.collection.bodySite
  • Type PractitionerRole changed from CodeableConcept to CodeableReference
Specimen.processing.method
  • Renamed from procedure to method
Specimen.collection.duration Specimen.processing.performer
  • Added Element
Specimen.collection.fastingStatus[x] Specimen.processing.device[x]
  • Added Element
Specimen.processing.additive
  • Type changed from Reference(Substance) to CodeableReference
Specimen.processing.time[x]
  • Add Type Duration
Specimen.condition Specimen.container.device[x]
  • Added Mandatory Element
Specimen.condition
  • Remove Binding `http://terminology.hl7.org/ValueSet/v2-0493` (extensible)
Specimen.accessionIdentifier
  • Deleted (-> Specimen.identifier (along with all the other identifiers))
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 for R4 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). ) for R4B as XML or JSON .

 

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

10.7.3.1 10.6.4.1 Terminology Bindings

Specimen.type Specimen.processing.procedure Specimen.container.type Specimen.container.additive[x]
Path Definition ValueSet Type Reference Documentation
Specimen.status SpecimenStatus Required

Codes providing the status/availability of a specimen.

Specimen.type Hl7VSSpecimenType icon (a valid code from specimenType icon ) Required Example

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.

Specimen.combined SpecimenStatus SpecimenCombined Required

Codes providing the combined status of a specimen.

Specimen.role SpecimenRole Preferred The type of

Codes providing the role of a specimen.

Specimen.feature.type SNOMEDCTBodyStructures Example v2.0487

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

Specimen.collection.method FHIRSpecimenCollectionMethod Example The technique

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

Specimen.collection.device[x] SpecimenContainer Example FHIRSpecimenCollectionMethod

Containers which may hold specimens or specimen containers. Include codes SNOMED CT(http://snomed.info/sct) where concept is-a 434711009 (Specimen container (physical object))

Specimen.collection.bodySite Codes describing anatomical locations. May include laterality. SNOMEDCTBodyStructures Example SNOMEDCTBodyStructures

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

Specimen.collection.fastingStatus[x] Codes describing the fasting status of the patient. Hl7VSRelevantClincialInformation icon (a valid code from relevantClincialInformation icon ) Extensible v2.0916

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.

Specimen.processing.method SpecimenProcessingMethod Example Type indicating the

The technique that is used to perform the process or preserve the specimen. These are codes from SNOMED CT - provided as an exemplar value set.

Specimen.processing.device[x] ProcessingDeviceCode Example SpecimenProcessingProcedure

Codes for devices used in specimen processing.

Specimen.container.device[x] Type of specimen container. ContainerDeviceCode Example SpecimenContainer

Codes for specimen container devices.

Specimen.condition Substance added to specimen container. Hl7VSSpecimenCondition icon (a valid code from specimenCondition icon ) Example v2.0371

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

10.6.4.2 Constraints

Specimen.condition Codes describing the state of the specimen. v2.0493
UniqueKey Level Extensible Location Description Expression
img  spm-1 Rule (base) Specimen.collection.collector SHALL only be present if Specimen.collection.procedure is not present collection.collector.empty() or collection.procedure.empty()

10.6.5 Notes:

10.6.5.1 Specimen Grouping

Specimens can be grouped at the Observation level via two ways:

  • A group at Observation.specimen with a reference to a group
  • By creating a group of specimens independent of observations
Additionally, a parent specimen can have multiple child specimens.

10.6.5.2 Specimen Searching

Specimens can be searched by parent, as described here . Additionally, a recursive, child-based search could be performed, using the instructions here . Note that recursive or reverse searching is highly dependent on the configuration of the local system(s) involved.

10.7.4 10.6.6 Search Parameters

Search parameters for this resource. See also the full list of search parameters for this resource , and check the Extensions registry for search parameters on extensions related to this resource. The common parameters also apply. See Searching for more information about searching in REST, messaging, and services.

The kind of specimen container Specimen.container.type container-id
Name Type Description Expression In Common
accession bodysite token reference The accession number associated with the specimen Reference to a resource (by instance) Specimen.accessionIdentifier Specimen.collection.bodySite.reference
bodysite collected token date The code for the body site from where date the specimen originated was collected Specimen.collection.bodySite Specimen.collection.collected.ofType(dateTime) | Specimen.collection.collected.ofType(Period)
collection-device-code collected date token The date code associated with the specimen was collected collection device Specimen.collection.collected Specimen.collection.device.ofType(CodeableConcept)
collector reference Who collected the specimen Specimen.collection.collector
( Practitioner , Organization , Patient , PractitionerRole , RelatedPerson )
container token container-device-code token The unique identifier code associated with the specimen container Specimen.container.identifier Specimen.container.device.ofType(CodeableConcept)
identifier token The unique identifier associated with the specimen Specimen.identifier 58 Resources
parent reference The parent of the specimen Specimen.parent
( Specimen )
patient reference The patient the specimen comes from Specimen.subject.where(resolve() is Patient)
( Patient ) 		60 Resources
procedure reference The procedure that collected the specimen Specimen.collection.procedure
( Procedure )
processing-device-code token The code associated with the processing device Specimen.processing.device.ofType(CodeableConcept)
request reference The request/order associated with the specimen Specimen.request
( ServiceRequest )
status token available | unavailable | unsatisfactory | entered-in-error Specimen.status
subject reference The subject of the specimen Specimen.subject
( Group , BiologicallyDerivedProduct , NutritionProduct , Device , Patient , Substance , Location )
type token The specimen type Specimen.type 10 Resources