DSTU2 FHIR Release 3 (STU)

This page is part of the FHIR Specification (v1.0.2: DSTU (v3.0.2: STU 2). 3). 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 R3 R2

4.25 10.6 Resource Specimen - Content

Orders and Observations Work Group Maturity Level : 1 2   Trial Use Compartments : Device , Patient , Practitioner

A sample to be used for analysis.

4.25.1 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 , 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.

4.25.2 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, biobanking, 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 DiagnosticOrder , DiagnosticReport , Media and , Observation , ProcedureRequest and Sequence

4.25.3 10.6.3 Resource Content

Structure

parent 0..* Reference ( Specimen ) Specimen from which this specimen originated Identifier assigned by the lab 0..1 dateTime The time when comment 0..* string Collector comments Treatment
Name Flags Card. Type Description & Constraints doco
. . Specimen 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 )
. . . type Σ 0..1 CodeableConcept Kind of material that forms the specimen
v2 Specimen Type ( Example )
. . . subject Σ 1..1 Reference ( Patient | Group | Device | Substance ) Where the specimen came from. This may be from the patient(s) or from the environment or a device
. . accessionIdentifier . receivedTime Σ 0..1 Identifier dateTime The time when specimen was received for processing
. . receivedTime . parent Σ 0..* Reference ( Specimen ) Specimen from which this specimen originated
. . . request 0..* Reference ( ProcedureRequest ) Why the specimen was received for processing collected
. . . collection 0..1 BackboneElement Collection details
. . . . collector Σ 0..1 Reference ( Practitioner ) Who collected the specimen
. . . . collected[x] Σ 0..1 Collection time
. . . . . collectedDateTime dateTime
. . . . . collectedPeriod Period
. . . . quantity 0..1 SimpleQuantity The quantity of specimen collected
. . . . method 0..1 CodeableConcept Technique used to perform collection
SpecimenCollectionMethod FHIR Specimen Collection Method ( Example )
. . . . bodySite 0..1 CodeableConcept Anatomical collection site
SNOMED CT Body Structures ( Example )
. . treatment . processing 0..* BackboneElement Processing and processing step details
. . . . description 0..1 string Textual description of procedure
. . . . procedure 0..1 CodeableConcept Indicates the treatment or processing step applied to the specimen
SpecimenTreatmentProcedure SpecimenProcessingProcedure ( 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 0..1 string Textual description of the container
. . . . type 0..1 CodeableConcept Kind of container directly associated with specimen
SpecimenContainer ( Example )
. . . . capacity 0..1 SimpleQuantity Container volume or size
. . . . specimenQuantity 0..1 SimpleQuantity Quantity of specimen within container
. . . . additive[x] 0..1 Additive associated with container
v2 Additive/Preservative ( Example )
. . . . . additiveCodeableConcept CodeableConcept
. . . . . additiveReference Reference ( Substance )
. . . note 0..* Annotation Comments

doco Documentation for this format

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] « Codes providing the status/availability of a specimen. (Strength=Required) SpecimenStatus ! » The kind of material that forms the specimen type : CodeableConcept [0..1] « The type of the specimen. (Strength=Example) v2 Specimen Type ?? » 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 » Where the specimen came from. This may be from the patient(s) or from the environment or a device subject : Reference [1..1] « Patient | Group | Device | Substance » 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] Time when specimen was received for processing or testing receivedTime : dateTime [0..1] Collection 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 Person who collected the Details concerning a test or procedure request that required a specimen to be collected collector request : Reference [0..1] « Practitioner [0..*] ProcedureRequest » To communicate any details or issues encountered about the specimen or during the specimen collection procedure collection. (for example: broken vial, sent with patient, frozen) comment note : string Annotation [0..*] Collection Person who collected the specimen collector : Reference [0..1] Practitioner Time when specimen was collected from subject - the physiologically relevant time collected[x] : Type [0..1] « dateTime | Period » 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 that is used to perform the procedure (Strength=Example) SpecimenCollectionMethod FHIR Specimen Collection Meth... ?? » 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 [0..1] « Codes describing anatomical locations. May include laterality. (Strength=Example) SNOMED CT Body Structures ?? » Treatment Processing Textual description of procedure description : string [0..1] A coded value specifying the procedure used to process the specimen procedure : CodeableConcept [0..1] « Type indicating the technique used to process the specimen (Strength=Example) SpecimenTreatmentProcedure SpecimenProcessingProcedure ?? » 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] : Type [0..1] dateTime | Period Container Id for container. There may be multiple; a manufacturer's bar code, lab assigned identifier, etc. The container ID may differ from the specimen id in some circumstances identifier : Identifier [0..*] Textual description of the container description : string [0..1] The type of container associated with the specimen (e.g. slide, aliquot, etc.) type : CodeableConcept [0..1] « Type of specimen container (Strength=Example) SpecimenContainer ?? » 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 or enhance the specimen. Examples: Formalin, Citrate, EDTA additive[x] : Type [0..1] « CodeableConcept | Reference ( Substance ); Substance added to specimen container (Strength=Example) v2 Additive/Preservative ?? » Details concerning the specimen collection collection [0..1] Details concerning treatment processing and processing steps for the specimen treatment 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>
 <
 <</type>
 <</parent>
 <</subject>
 <</accessionIdentifier>
 <
 <
  <</collector>
  <
  <</collected[x]>
  <</quantity>
  <</method>
  <</bodySite>

 <identifier><!-- 0..* Identifier External Identifier --></identifier>
 <accessionIdentifier><!-- 0..1 Identifier Identifier assigned by the lab --></accessionIdentifier>
 <status value="[code]"/><!-- 0..1 available | unavailable | unsatisfactory | entered-in-error -->
 <type><!-- 0..1 CodeableConcept Kind of material that forms the specimen --></type>
 <subject><!-- 1..1 Reference(Patient|Group|Device|Substance) Where the specimen came from. This may be from the patient(s) or from the environment or a device --></subject>
 <receivedTime value="[dateTime]"/><!-- 0..1 The time when specimen was received for processing -->
 <parent><!-- 0..* Reference(Specimen) Specimen from which this specimen originated --></parent>
 <request><!-- 0..* Reference(ProcedureRequest) Why the specimen was collected --></request>
 <collection>  <!-- 0..1 Collection details -->
  <collector><!-- 0..1 Reference(Practitioner) Who collected the specimen --></collector>
  <collected[x]><!-- 0..1 dateTime|Period Collection time --></collected[x]>
  <quantity><!-- 0..1 Quantity(SimpleQuantity) The quantity of specimen collected --></quantity>
  <method><!-- 0..1 CodeableConcept Technique used to perform collection --></method>
  <bodySite><!-- 0..1 CodeableConcept Anatomical collection site --></bodySite>

 </collection>
 <
  <
  <</procedure>
  <</additive>
 </treatment>
 <
  <</identifier>
  <
  <</type>
  <</capacity>
  <</specimenQuantity>
  <</additive[x]>

 <processing>  <!-- 0..* Processing and processing step details -->
  <description value="[string]"/><!-- 0..1 Textual description of procedure -->
  <procedure><!-- 0..1 CodeableConcept Indicates the treatment step  applied to the specimen --></procedure>
  <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><!-- 0..* Identifier Id for the container --></identifier>
  <description value="[string]"/><!-- 0..1 Textual description of the container -->
  <type><!-- 0..1 CodeableConcept Kind of container directly associated with specimen --></type>
  <capacity><!-- 0..1 Quantity(SimpleQuantity) Container volume or size --></capacity>
  <specimenQuantity><!-- 0..1 Quantity(SimpleQuantity) Quantity of specimen within container --></specimenQuantity>
  <additive[x]><!-- 0..1 CodeableConcept|Reference(Substance) Additive associated with container --></additive[x]>

 </container>
 <note><!-- 0..* Annotation Comments --></note>

</Specimen>

JSON Template 

{
  "resourceType" : "",

{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
  "subject" : { Reference(Patient|Group|Device|Substance) }, // R!  Where the specimen came from. This may be from the patient(s) or from the environment or a device
  "receivedTime" : "<dateTime>", // The time when specimen was received for processing
  "parent" : [{ Reference(Specimen) }], // Specimen from which this specimen originated
  "request" : [{ Reference(ProcedureRequest) }], // Why the specimen was collected
  "collection" : { // Collection details
    "collector" : { Reference(Practitioner) }, // Who collected the specimen

    // collected[x]: Collection time. One of these 2:
    ">",
    " },
    "
    "
    "

    "collectedDateTime" : "<dateTime>",
    "collectedPeriod" : { Period },
    "quantity" : { Quantity(SimpleQuantity) }, // The quantity of specimen collected
    "method" : { CodeableConcept }, // Technique used to perform collection
    "bodySite" : { CodeableConcept } // Anatomical collection site

  },
  "
    "
    "
    "

  "processing" : [{ // Processing and processing step details
    "description" : "<string>", // Textual description of procedure
    "procedure" : { 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.)
    "identifier" : [{ Identifier }], // Id for the container
    "description" : "<string>", // Textual description of the container
    "type" : { CodeableConcept }, // Kind of container directly associated with specimen
    "capacity" : { Quantity(SimpleQuantity) }, // Container volume or size
    "specimenQuantity" : { Quantity(SimpleQuantity) }, // Quantity of specimen within container

    // additive[x]: Additive associated with container. One of these 2:
    " }
    " }
  }]

    "additiveCodeableConcept" : { CodeableConcept }
    "additiveReference" : { Reference(Substance) }
  }],
  "note" : [{ Annotation }] // Comments

}

Turtle Template 


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


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

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:Specimen.identifier [ Identifier ], ... ; # 0..* External Identifier
  fhir:Specimen.accessionIdentifier [ Identifier ]; # 0..1 Identifier assigned by the lab
  fhir:Specimen.status [ code ]; # 0..1 available | unavailable | unsatisfactory | entered-in-error
  fhir:Specimen.type [ CodeableConcept ]; # 0..1 Kind of material that forms the specimen
  fhir:Specimen.subject [ Reference(Patient|Group|Device|Substance) ]; # 1..1 Where the specimen came from. This may be from the patient(s) or from the environment or a device
  fhir:Specimen.receivedTime [ dateTime ]; # 0..1 The time when specimen was received for processing
  fhir:Specimen.parent [ Reference(Specimen) ], ... ; # 0..* Specimen from which this specimen originated
  fhir:Specimen.request [ Reference(ProcedureRequest) ], ... ; # 0..* Why the specimen was collected
  fhir:Specimen.collection [ # 0..1 Collection details
    fhir:Specimen.collection.collector [ Reference(Practitioner) ]; # 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.quantity [ Quantity(SimpleQuantity) ]; # 0..1 The quantity of specimen collected
    fhir:Specimen.collection.method [ CodeableConcept ]; # 0..1 Technique used to perform collection
    fhir:Specimen.collection.bodySite [ CodeableConcept ]; # 0..1 Anatomical collection site
  ];
  fhir:Specimen.processing [ # 0..* Processing and processing step details
    fhir:Specimen.processing.description [ string ]; # 0..1 Textual description of procedure
    fhir:Specimen.processing.procedure [ CodeableConcept ]; # 0..1 Indicates the treatment step  applied to the specimen
    fhir:Specimen.processing.additive [ Reference(Substance) ], ... ; # 0..* Material used in the processing step
    # Specimen.processing.time[x] : 0..1 Date and time of specimen processing. One of these 2
      fhir:Specimen.processing.timeDateTime [ dateTime ]
      fhir:Specimen.processing.timePeriod [ Period ]
  ], ...;
  fhir:Specimen.container [ # 0..* Direct container of specimen (tube/slide, etc.)
    fhir:Specimen.container.identifier [ Identifier ], ... ; # 0..* Id for the container
    fhir:Specimen.container.description [ string ]; # 0..1 Textual description of the container
    fhir:Specimen.container.type [ CodeableConcept ]; # 0..1 Kind of container directly associated with specimen
    fhir:Specimen.container.capacity [ Quantity(SimpleQuantity) ]; # 0..1 Container volume or size
    fhir:Specimen.container.specimenQuantity [ Quantity(SimpleQuantity) ]; # 0..1 Quantity of specimen within container
    # Specimen.container.additive[x] : 0..1 Additive associated with container. One of these 2
      fhir:Specimen.container.additiveCodeableConcept [ CodeableConcept ]
      fhir:Specimen.container.additiveReference [ Reference(Substance) ]
  ], ...;
  fhir:Specimen.note [ Annotation ], ... ; # 0..* Comments
]

Changes since DSTU2

Specimen
Specimen.request
  • Added Element
Specimen.processing
  • Added Element
Specimen.processing.description
  • Added Element
Specimen.processing.procedure
  • Added Element
Specimen.processing.additive
  • Added Element
Specimen.processing.time[x]
  • Added Element
Specimen.note
  • Added Element
Specimen.collection.comment
  • deleted
Specimen.treatment
  • deleted

See the Full Difference for further information

This analysis is available as XML or JSON .

See R2 <--> R3 Conversion Maps (status = 6 tests that all execute ok. All tests pass round-trip testing and 1 r3 resources are invalid (1 errors). ).

Structure

parent 0..* Reference ( Specimen ) Specimen from which this specimen originated Identifier assigned by the lab 0..1 dateTime The time when comment 0..* string Collector comments Treatment
Name Flags Card. Type Description & Constraints doco
. . Specimen 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 )
. . . type Σ 0..1 CodeableConcept Kind of material that forms the specimen
v2 Specimen Type ( Example )
. . . subject Σ 1..1 Reference ( Patient | Group | Device | Substance ) Where the specimen came from. This may be from the patient(s) or from the environment or a device
. . accessionIdentifier . receivedTime Σ 0..1 Identifier dateTime The time when specimen was received for processing
. . receivedTime . parent Σ 0..* Reference ( Specimen ) Specimen from which this specimen originated
. . . request 0..* Reference ( ProcedureRequest ) Why the specimen was received for processing collected
. . . collection 0..1 BackboneElement Collection details
. . . . collector Σ 0..1 Reference ( Practitioner ) Who collected the specimen
. . . . collected[x] Σ 0..1 Collection time
. . . . . collectedDateTime dateTime
. . . . . collectedPeriod Period
. . . . quantity 0..1 SimpleQuantity The quantity of specimen collected
. . . . method 0..1 CodeableConcept Technique used to perform collection
SpecimenCollectionMethod FHIR Specimen Collection Method ( Example )
. . . . bodySite 0..1 CodeableConcept Anatomical collection site
SNOMED CT Body Structures ( Example )
. . treatment . processing 0..* BackboneElement Processing and processing step details
. . . . description 0..1 string Textual description of procedure
. . . . procedure 0..1 CodeableConcept Indicates the treatment or processing step applied to the specimen
SpecimenTreatmentProcedure SpecimenProcessingProcedure ( 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 0..1 string Textual description of the container
. . . . type 0..1 CodeableConcept Kind of container directly associated with specimen
SpecimenContainer ( Example )
. . . . capacity 0..1 SimpleQuantity Container volume or size
. . . . specimenQuantity 0..1 SimpleQuantity Quantity of specimen within container
. . . . additive[x] 0..1 Additive associated with container
v2 Additive/Preservative ( Example )
. . . . . additiveCodeableConcept CodeableConcept
. . . . . additiveReference Reference ( Substance )
. . . note 0..* Annotation Comments

doco Documentation for this format

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] « Codes providing the status/availability of a specimen. (Strength=Required) SpecimenStatus ! » The kind of material that forms the specimen type : CodeableConcept [0..1] « The type of the specimen. (Strength=Example) v2 Specimen Type ?? » 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 » Where the specimen came from. This may be from the patient(s) or from the environment or a device subject : Reference [1..1] « Patient | Group | Device | Substance » 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] Time when specimen was received for processing or testing receivedTime : dateTime [0..1] Collection 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 Person who collected the Details concerning a test or procedure request that required a specimen to be collected collector request : Reference [0..1] « Practitioner [0..*] ProcedureRequest » To communicate any details or issues encountered about the specimen or during the specimen collection procedure collection. (for example: broken vial, sent with patient, frozen) comment note : string Annotation [0..*] Collection Person who collected the specimen collector : Reference [0..1] Practitioner Time when specimen was collected from subject - the physiologically relevant time collected[x] : Type [0..1] « dateTime | Period » 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 that is used to perform the procedure (Strength=Example) SpecimenCollectionMethod FHIR Specimen Collection Meth... ?? » 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 [0..1] « Codes describing anatomical locations. May include laterality. (Strength=Example) SNOMED CT Body Structures ?? » Treatment Processing Textual description of procedure description : string [0..1] A coded value specifying the procedure used to process the specimen procedure : CodeableConcept [0..1] « Type indicating the technique used to process the specimen (Strength=Example) SpecimenTreatmentProcedure SpecimenProcessingProcedure ?? » 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] : Type [0..1] dateTime | Period Container Id for container. There may be multiple; a manufacturer's bar code, lab assigned identifier, etc. The container ID may differ from the specimen id in some circumstances identifier : Identifier [0..*] Textual description of the container description : string [0..1] The type of container associated with the specimen (e.g. slide, aliquot, etc.) type : CodeableConcept [0..1] « Type of specimen container (Strength=Example) SpecimenContainer ?? » 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 or enhance the specimen. Examples: Formalin, Citrate, EDTA additive[x] : Type [0..1] « CodeableConcept | Reference ( Substance ); Substance added to specimen container (Strength=Example) v2 Additive/Preservative ?? » Details concerning the specimen collection collection [0..1] Details concerning treatment processing and processing steps for the specimen treatment 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>
 <
 <</type>
 <</parent>
 <</subject>
 <</accessionIdentifier>
 <
 <
  <</collector>
  <
  <</collected[x]>
  <</quantity>
  <</method>
  <</bodySite>

 <identifier><!-- 0..* Identifier External Identifier --></identifier>
 <accessionIdentifier><!-- 0..1 Identifier Identifier assigned by the lab --></accessionIdentifier>
 <status value="[code]"/><!-- 0..1 available | unavailable | unsatisfactory | entered-in-error -->
 <type><!-- 0..1 CodeableConcept Kind of material that forms the specimen --></type>
 <subject><!-- 1..1 Reference(Patient|Group|Device|Substance) Where the specimen came from. This may be from the patient(s) or from the environment or a device --></subject>
 <receivedTime value="[dateTime]"/><!-- 0..1 The time when specimen was received for processing -->
 <parent><!-- 0..* Reference(Specimen) Specimen from which this specimen originated --></parent>
 <request><!-- 0..* Reference(ProcedureRequest) Why the specimen was collected --></request>
 <collection>  <!-- 0..1 Collection details -->
  <collector><!-- 0..1 Reference(Practitioner) Who collected the specimen --></collector>
  <collected[x]><!-- 0..1 dateTime|Period Collection time --></collected[x]>
  <quantity><!-- 0..1 Quantity(SimpleQuantity) The quantity of specimen collected --></quantity>
  <method><!-- 0..1 CodeableConcept Technique used to perform collection --></method>
  <bodySite><!-- 0..1 CodeableConcept Anatomical collection site --></bodySite>

 </collection>
 <
  <
  <</procedure>
  <</additive>
 </treatment>
 <
  <</identifier>
  <
  <</type>
  <</capacity>
  <</specimenQuantity>
  <</additive[x]>

 <processing>  <!-- 0..* Processing and processing step details -->
  <description value="[string]"/><!-- 0..1 Textual description of procedure -->
  <procedure><!-- 0..1 CodeableConcept Indicates the treatment step  applied to the specimen --></procedure>
  <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><!-- 0..* Identifier Id for the container --></identifier>
  <description value="[string]"/><!-- 0..1 Textual description of the container -->
  <type><!-- 0..1 CodeableConcept Kind of container directly associated with specimen --></type>
  <capacity><!-- 0..1 Quantity(SimpleQuantity) Container volume or size --></capacity>
  <specimenQuantity><!-- 0..1 Quantity(SimpleQuantity) Quantity of specimen within container --></specimenQuantity>
  <additive[x]><!-- 0..1 CodeableConcept|Reference(Substance) Additive associated with container --></additive[x]>

 </container>
 <note><!-- 0..* Annotation Comments --></note>

</Specimen>

JSON Template 

{
  "resourceType" : "",

{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
  "subject" : { Reference(Patient|Group|Device|Substance) }, // R!  Where the specimen came from. This may be from the patient(s) or from the environment or a device
  "receivedTime" : "<dateTime>", // The time when specimen was received for processing
  "parent" : [{ Reference(Specimen) }], // Specimen from which this specimen originated
  "request" : [{ Reference(ProcedureRequest) }], // Why the specimen was collected
  "collection" : { // Collection details
    "collector" : { Reference(Practitioner) }, // Who collected the specimen

    // collected[x]: Collection time. One of these 2:
    ">",
    " },
    "
    "
    "

    "collectedDateTime" : "<dateTime>",
    "collectedPeriod" : { Period },
    "quantity" : { Quantity(SimpleQuantity) }, // The quantity of specimen collected
    "method" : { CodeableConcept }, // Technique used to perform collection
    "bodySite" : { CodeableConcept } // Anatomical collection site

  },
  "
    "
    "
    "

  "processing" : [{ // Processing and processing step details
    "description" : "<string>", // Textual description of procedure
    "procedure" : { 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.)
    "identifier" : [{ Identifier }], // Id for the container
    "description" : "<string>", // Textual description of the container
    "type" : { CodeableConcept }, // Kind of container directly associated with specimen
    "capacity" : { Quantity(SimpleQuantity) }, // Container volume or size
    "specimenQuantity" : { Quantity(SimpleQuantity) }, // Quantity of specimen within container

    // additive[x]: Additive associated with container. One of these 2:
    " }
    " }
  }]

    "additiveCodeableConcept" : { CodeableConcept }
    "additiveReference" : { Reference(Substance) }
  }],
  "note" : [{ Annotation }] // Comments

}

Turtle Template 


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


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

  # from Resource: .id, .meta, .implicitRules, and .language
  # from DomainResource: .text, .contained, .extension, and .modifierExtension
  fhir:Specimen.identifier [ Identifier ], ... ; # 0..* External Identifier
  fhir:Specimen.accessionIdentifier [ Identifier ]; # 0..1 Identifier assigned by the lab
  fhir:Specimen.status [ code ]; # 0..1 available | unavailable | unsatisfactory | entered-in-error
  fhir:Specimen.type [ CodeableConcept ]; # 0..1 Kind of material that forms the specimen
  fhir:Specimen.subject [ Reference(Patient|Group|Device|Substance) ]; # 1..1 Where the specimen came from. This may be from the patient(s) or from the environment or a device
  fhir:Specimen.receivedTime [ dateTime ]; # 0..1 The time when specimen was received for processing
  fhir:Specimen.parent [ Reference(Specimen) ], ... ; # 0..* Specimen from which this specimen originated
  fhir:Specimen.request [ Reference(ProcedureRequest) ], ... ; # 0..* Why the specimen was collected
  fhir:Specimen.collection [ # 0..1 Collection details
    fhir:Specimen.collection.collector [ Reference(Practitioner) ]; # 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.quantity [ Quantity(SimpleQuantity) ]; # 0..1 The quantity of specimen collected
    fhir:Specimen.collection.method [ CodeableConcept ]; # 0..1 Technique used to perform collection
    fhir:Specimen.collection.bodySite [ CodeableConcept ]; # 0..1 Anatomical collection site
  ];
  fhir:Specimen.processing [ # 0..* Processing and processing step details
    fhir:Specimen.processing.description [ string ]; # 0..1 Textual description of procedure
    fhir:Specimen.processing.procedure [ CodeableConcept ]; # 0..1 Indicates the treatment step  applied to the specimen
    fhir:Specimen.processing.additive [ Reference(Substance) ], ... ; # 0..* Material used in the processing step
    # Specimen.processing.time[x] : 0..1 Date and time of specimen processing. One of these 2
      fhir:Specimen.processing.timeDateTime [ dateTime ]
      fhir:Specimen.processing.timePeriod [ Period ]
  ], ...;
  fhir:Specimen.container [ # 0..* Direct container of specimen (tube/slide, etc.)
    fhir:Specimen.container.identifier [ Identifier ], ... ; # 0..* Id for the container
    fhir:Specimen.container.description [ string ]; # 0..1 Textual description of the container
    fhir:Specimen.container.type [ CodeableConcept ]; # 0..1 Kind of container directly associated with specimen
    fhir:Specimen.container.capacity [ Quantity(SimpleQuantity) ]; # 0..1 Container volume or size
    fhir:Specimen.container.specimenQuantity [ Quantity(SimpleQuantity) ]; # 0..1 Quantity of specimen within container
    # Specimen.container.additive[x] : 0..1 Additive associated with container. One of these 2
      fhir:Specimen.container.additiveCodeableConcept [ CodeableConcept ]
      fhir:Specimen.container.additiveReference [ Reference(Substance) ]
  ], ...;
  fhir:Specimen.note [ Annotation ], ... ; # 0..* Comments
]

  Changes since DSTU2

Specimen
Specimen.request
  • Added Element
Specimen.processing
  • Added Element
Specimen.processing.description
  • Added Element
Specimen.processing.procedure
  • Added Element
Specimen.processing.additive
  • Added Element
Specimen.processing.time[x]
  • Added Element
Specimen.note
  • Added Element
Specimen.collection.comment
  • deleted
Specimen.treatment
  • deleted

See the Full Difference for further information

This analysis is available as XML or JSON .

See R2 <--> R3 Conversion Maps (status = 6 tests that all execute ok. All tests pass round-trip testing and 1 r3 resources are invalid (1 errors). ).

 

Alternate definitions: Schema / Schematron , Resource Profile Master Definition ( XML , JSON ), Questionnaire XML Schema / Schematron (for ) + JSON Schema , ShEx (for Turtle )

4.25.3.1 10.6.3.1 Terminology Bindings

Specimen.treatment.procedure
Path Definition Type Reference
Specimen.status Codes providing the status/availability of a specimen. Required SpecimenStatus
Specimen.type The type of the specimen. Example v2 Specimen Type
Specimen.collection.method The technique that is used to perform the procedure Example SpecimenCollectionMethod FHIR Specimen Collection Method
Specimen.collection.bodySite Codes describing anatomical locations. May include laterality. Example SNOMED CT Body Structures
Specimen.processing.procedure Type indicating the technique used to process the specimen Example SpecimenTreatmentProcedure SpecimenProcessingProcedure
Specimen.container.type Type of specimen container Example SpecimenContainer
Specimen.container.additive[x] Substance added to specimen container Example v2 Additive/Preservative

4.25.4 10.6.4 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 Paths Expression In Common
accession token The accession number associated with the specimen Specimen.accessionIdentifier
bodysite token The code for the body site from where the specimen originated Specimen.collection.bodySite
collected date The date the specimen was collected Specimen.collection.collected[x] Specimen.collection.collected
collector reference Who collected the specimen Specimen.collection.collector
( Practitioner )
container token The kind of specimen container Specimen.container.type
container-id token The unique identifier associated with the specimen container Specimen.container.identifier
identifier token The unique identifier associated with the specimen Specimen.identifier
parent reference The parent of the specimen Specimen.parent
( Specimen )
patient reference The patient the specimen comes from Specimen.subject
( Patient )
status token available | unavailable | unsatisfactory | entered-in-error Specimen.status
subject reference The subject of the specimen Specimen.subject
( Group , Device , Patient , Substance , Group )
type token The specimen type Specimen.type