Release 4B 5 Ballot

This page is part of the FHIR Specification (v4.3.0: R4B (v5.0.0-ballot: R5 Ballot - STU see ballot notes ). The current version which supercedes this version is 5.0.0 . For a full list of available versions, see the Directory of published versions . Page versions: R5 R4B R4 R3 R2

10.7 10.8 Resource Specimen - Content

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

A sample to be used for analysis.

10.7.1 10.8.1 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 10.8.2 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.

10.7.3 10.8.3 References to this Resource

This resource is referenced by

10.7.4 10.8.4 Resource Content

Structure

Name Flags Card. Type Description & Constraints doco
. . Specimen TU DomainResource Sample for analysis

Elements defined in Ancestors: id , meta , implicitRules , language , text , contained , extension , modifierExtension
. . . identifier Σ 0..* Identifier External Identifier

. . . accessionIdentifier Σ 0..1 Identifier Identifier assigned by the lab
. . . status ?! Σ 0..1 code available | unavailable | unsatisfactory | entered-in-error
SpecimenStatus ( Required )
. . . subject Σ 0..1 Reference ( 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 substance, a biologically-derived product, or a device
. . . 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

. . . combined Σ 0..1 code grouped | pooled
SpecimenCombined ( Required )
... role 0..* CodeableConcept The role the specimen serves
SpecimenRole ( Preferred )

. . . collection feature 0..1 0..* BackboneElement The physical feature of a specimen

.... type 1..1 CodeableConcept Highlighted feature
SNOMED CT Body Structures ( Example )
.... description 1..1 string Information about the feature
... collection 0..1 BackboneElement Collection details
. . . . collector Σ 0..1 Reference ( 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
FHIR Specimen Collection Method ( Example )
. . . . device 0..1 CodeableReference ( Device ) Device used to perform collection
SpecimenCollectionDevice ( Example )
. . . bodySite . procedure 0..1 CodeableConcept Reference ( Procedure ) The procedure that collects the specimen
.... bodySite 0..1 CodeableReference ( BodyStructure ) Anatomical collection site
SNOMED CT Body Structures ( Example )
. . . . fastingStatus[x] Σ 0..1 Whether or how long patient abstained from food and/or drink
hl7VS-relevantClincialInformation icon ( 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
SpecimenProcessingProcedure SpecimenProcessingMethod ( Example )
. . . . additive 0..* Reference ( Substance ) Material used in the processing step

. . . . time[x] 0..1 Date and time of specimen processing
. . . . . timeDateTime dateTime
. . . . . timePeriod Period
. . . container 0..* BackboneElement Direct container of specimen (tube/slide, etc.)
identifier Σ 0..* Identifier Id for the container
. . . description . device 0..1 1..1 string Reference ( Device ) Textual description of Device resource for the container
. . . type . location 0..1 CodeableConcept Reference ( Location ) Kind of Where the container directly associated with specimen is
SpecimenContainer ( Example )
. . . . capacity specimenQuantity 0..1 SimpleQuantity Container volume or size specimenQuantity 0..1 SimpleQuantity Quantity of specimen within container additive[x] 0..1 Additive associated with container
hl7VS-additivePreservative ( Example ) additiveCodeableConcept CodeableConcept additiveReference Reference ( Substance )
. . . condition Σ 0..* CodeableConcept State of the specimen
hl7VS-specimenCondition icon ( Extensible )

. . . note 0..* Annotation Comments


doco Documentation for this format

See the Extensions for this resource

UML Diagram ( Legend )

Specimen ( DomainResource ) Id for specimen identifier : 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 procedures accessionIdentifier : 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 specimen type : 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 substance, a biologically-derived product, or a device subject : Reference [0..1] « Patient | Group | Device | BiologicallyDerivedProduct | Substance | Location » 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..*] « null (Strength=Preferred) SpecimenRole ? » A mode or state of being that describes the nature of the specimen condition : 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..*] Feature The landmark or feature being highlighted type : CodeableConcept [1..1] « null (Strength=Example) SNOMEDCTBodyStructures ?? » Description of the feature of the specimen description : string [1..1] Collection Person who collected the specimen collector : Reference [0..1] « Practitioner | PractitionerRole | Patient | RelatedPerson » Time when specimen was collected from subject - the physiologically relevant time collected[x] : Element 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] « null (Strength=Example) FHIRSpecimenCollectionMethod ?? » A coded value specifying the technique that is used to perform the procedure device : 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 specimens bodySite : CodeableConcept 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 collection fastingStatus[x] : Element DataType [0..1] « CodeableConcept | Duration ; null (Strength=Extensible) 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] « null (Strength=Example) SpecimenProcessingProcedure SpecimenProcessingMethod ?? » Material used in the processing step additive : 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 formalin time[x] : Element DataType [0..1] « dateTime | Period » 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 in some circumstances identifier : Identifier [0..*] Textual description of specimen. If the container is in a holder then the referenced device will point to a parent device description device : string Reference [0..1] [1..1] « Device » The type location of the container associated with holding the specimen (e.g. slide, aliquot, etc.) type location : CodeableConcept Reference [0..1] « null (Strength=Example) SpecimenContainer Location ?? » 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 specimen. Examples: Formalin, Citrate, EDTA additive[x] : Element [0..1] « CodeableConcept | Reference ( Substance ); null (Strength=Example) 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 Hl7VSAdditivePreservative ?? » [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><!-- 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>
 <</subject>
 <

 <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>

  <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>
  <</bodySite>
  <</fastingStatus[x]>

  <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 -->
  <</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.) -->
  <</identifier>
  <
  <</type>
  <</capacity>

  <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>
  <</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 }], // 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:
  fhir:

  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:

    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:

    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:

    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:
    fhir:
    fhir:
    fhir:

    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
    # . One of these 2
      fhir: ]
      fhir:) ]

  ], ...;
  fhir:Specimen.condition [ CodeableConcept ], ... ; # 0..* State of the specimen
  fhir:Specimen.note [ Annotation ], ... ; # 0..* Comments
]

Changes since R4

Specimen
Specimen.subject
  • No Changes 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 .

Conversions between R3 and R4 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

Name Flags Card. Type Description & Constraints doco
. . Specimen TU DomainResource Sample for analysis

Elements defined in Ancestors: id , meta , implicitRules , language , text , contained , extension , modifierExtension
. . . identifier Σ 0..* Identifier External Identifier

. . . accessionIdentifier Σ 0..1 Identifier Identifier assigned by the lab
. . . status ?! Σ 0..1 code available | unavailable | unsatisfactory | entered-in-error
SpecimenStatus ( Required )
. . . subject Σ 0..1 Reference ( 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 substance, a biologically-derived product, or a device
. . . 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

. . . combined Σ 0..1 code grouped | pooled
SpecimenCombined ( Required )
... role 0..* CodeableConcept The role the specimen serves
SpecimenRole ( Preferred )

. . . collection feature 0..1 0..* BackboneElement The physical feature of a specimen

.... type 1..1 CodeableConcept Highlighted feature
SNOMED CT Body Structures ( Example )
.... description 1..1 string Information about the feature
... collection 0..1 BackboneElement Collection details
. . . . collector Σ 0..1 Reference ( 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
FHIR Specimen Collection Method ( Example )
. . . . device 0..1 CodeableReference ( Device ) Device used to perform collection
SpecimenCollectionDevice ( Example )
. . . bodySite . procedure 0..1 CodeableConcept Reference ( Procedure ) The procedure that collects the specimen
.... bodySite 0..1 CodeableReference ( BodyStructure ) Anatomical collection site
SNOMED CT Body Structures ( Example )
. . . . fastingStatus[x] Σ 0..1 Whether or how long patient abstained from food and/or drink
hl7VS-relevantClincialInformation icon ( 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
SpecimenProcessingProcedure SpecimenProcessingMethod ( Example )
. . . . additive 0..* Reference ( Substance ) Material used in the processing step

. . . . time[x] 0..1 Date and time of specimen processing
. . . . . timeDateTime dateTime
. . . . . timePeriod Period
. . . container 0..* BackboneElement Direct container of specimen (tube/slide, etc.)
identifier Σ 0..* Identifier Id for the container
. . . description . device 0..1 1..1 string Reference ( Device ) Textual description of Device resource for the container
. . . type . location 0..1 CodeableConcept Reference ( Location ) Kind of Where the container directly associated with specimen is
SpecimenContainer ( Example )
. . . . capacity specimenQuantity 0..1 SimpleQuantity Container volume or size specimenQuantity 0..1 SimpleQuantity Quantity of specimen within container additive[x] 0..1 Additive associated with container
hl7VS-additivePreservative ( Example ) additiveCodeableConcept CodeableConcept additiveReference Reference ( Substance )
. . . condition Σ 0..* CodeableConcept State of the specimen
hl7VS-specimenCondition icon ( Extensible )

. . . note 0..* Annotation Comments


doco Documentation for this format

See the Extensions for this resource

UML Diagram ( Legend )

Specimen ( DomainResource ) Id for specimen identifier : 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 procedures accessionIdentifier : 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 specimen type : 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 substance, a biologically-derived product, or a device subject : Reference [0..1] « Patient | Group | Device | BiologicallyDerivedProduct | Substance | Location » 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..*] « null (Strength=Preferred) SpecimenRole ? » A mode or state of being that describes the nature of the specimen condition : 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..*] Feature The landmark or feature being highlighted type : CodeableConcept [1..1] « null (Strength=Example) SNOMEDCTBodyStructures ?? » Description of the feature of the specimen description : string [1..1] Collection Person who collected the specimen collector : Reference [0..1] « Practitioner | PractitionerRole | Patient | RelatedPerson » Time when specimen was collected from subject - the physiologically relevant time collected[x] : Element 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] « null (Strength=Example) FHIRSpecimenCollectionMethod ?? » A coded value specifying the technique that is used to perform the procedure device : 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 specimens bodySite : CodeableConcept 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 collection fastingStatus[x] : Element DataType [0..1] « CodeableConcept | Duration ; null (Strength=Extensible) 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] « null (Strength=Example) SpecimenProcessingProcedure SpecimenProcessingMethod ?? » Material used in the processing step additive : 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 formalin time[x] : Element DataType [0..1] « dateTime | Period » 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 in some circumstances identifier : Identifier [0..*] Textual description of specimen. If the container is in a holder then the referenced device will point to a parent device description device : string Reference [0..1] [1..1] « Device » The type location of the container associated with holding the specimen (e.g. slide, aliquot, etc.) type location : CodeableConcept Reference [0..1] « null (Strength=Example) SpecimenContainer Location ?? » 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 specimen. Examples: Formalin, Citrate, EDTA additive[x] : Element [0..1] « CodeableConcept | Reference ( Substance ); null (Strength=Example) 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 Hl7VSAdditivePreservative ?? » [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><!-- 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>
 <</subject>
 <

 <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>

  <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>
  <</bodySite>
  <</fastingStatus[x]>

  <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 -->
  <</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.) -->
  <</identifier>
  <
  <</type>
  <</capacity>

  <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>
  <</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 }], // 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:
  fhir:

  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:

    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:

    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:

    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:
    fhir:
    fhir:
    fhir:

    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
    # . One of these 2
      fhir: ]
      fhir:) ]

  ], ...;
  fhir:Specimen.condition [ CodeableConcept ], ... ; # 0..* State of the specimen
  fhir:Specimen.note [ Annotation ], ... ; # 0..* Comments
]

Changes since Release 4

Specimen
Specimen.subject
  • No Changes 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 .

Conversions between R3 and R4 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). )

 

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

10.7.4.1 10.8.4.1 Terminology Bindings

Specimen.collection.method Specimen.collection.fastingStatus[x] Specimen.processing.procedure Specimen.container.type Specimen.container.additive[x]
Path Definition Type Reference
Specimen.status

Codes providing the status/availability of a specimen.

Required SpecimenStatus
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.

Example Hl7VSSpecimenType icon
Specimen.combined

Codes providing the combined status of a specimen.

Required SpecimenCombined
Specimen.role

Codes providing the role of a specimen.

Example Preferred FHIRSpecimenCollectionMethod SpecimenRole
Specimen.collection.bodySite 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)).

Example SNOMEDCTBodyStructures
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.

Extensible Example Hl7VSRelevantClincialInformation FHIRSpecimenCollectionMethod
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)).

Example SpecimenProcessingProcedure SNOMEDCTBodyStructures
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.

Example Extensible SpecimenContainer Hl7VSRelevantClincialInformation icon
Specimen.processing.method

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

Example Hl7VSAdditivePreservative SpecimenProcessingMethod
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.

Extensible Hl7VSSpecimenCondition icon

10.7.5 10.8.5 Search Parameters

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

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