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10.6 10.7 Resource Specimen - Content

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

A sample to be used for analysis.

10.6.1 10.7.1 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.

10.6.2 10.7.2 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, 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 References

This resource is referenced by DiagnosticReport , ImagingStudy , Media , MolecularSequence , Observation , ProcedureRequest ServiceRequest and Sequence itself.

This resource does not implement any patterns.

10.6.3 10.7.4 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 )
. . . type Σ 0..1 CodeableConcept Kind of material that forms the specimen
v2 Specimen Type ( Example )
. . . subject Σ 1..1 0..1 Reference ( Patient | Group | Device | Substance | Location ) Where the specimen came from. This may be from the patient(s) or patient(s), from a location (e.g., the environment source of an environmental sample), or a sampling of a substance or a device
. . . receivedTime Σ 0..1 dateTime The time when specimen was received for processing
. . . parent 0..* Reference ( Specimen ) Specimen from which this specimen originated
. . . request 0..* Reference ( ProcedureRequest ServiceRequest ) Why the specimen was collected
. . . collection 0..1 BackboneElement Collection details
. . . . collector Σ 0..1 Reference ( Practitioner | PractitionerRole ) 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 )
. . . . bodySite 0..1 CodeableConcept Anatomical collection site
SNOMED CT Body Structures ( Example )
. . . . fastingStatus[x] Σ 0..1 Whether or how long patient abstained from food and/or drink
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 0..1 CodeableConcept Indicates the treatment step applied to the specimen
SpecimenProcessingProcedure Specimen processing procedure ( 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 Specimen container ( 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 Additive ( Example )
. . . . . additiveCodeableConcept CodeableConcept
. . . . . additiveReference Reference ( Substance )
. . . condition Σ 0..* CodeableConcept State of the specimen
v2 Specimen Condition ( Extensible )
. . . 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 v2.0487 ?? » Where the specimen came from. This may be from the patient(s) or patient(s), from a location (e.g., the environment source of an environmental sample), or a sampling of a substance or a device subject : Reference [1..1] [0..1] « Patient | Group | Device | Substance | Location » Time when specimen was received 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 test or procedure service request that required a specimen to be collected request : Reference [0..*] ProcedureRequest « ServiceRequest » 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) v2.0493 + » 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..*] Collection Person who collected the specimen collector : Reference [0..1] « Practitioner | PractitionerRole » Time when specimen was collected from subject - the physiologically relevant time collected[x] : Type [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 that is used to perform the procedure procedure. (Strength=Example) FHIR Specimen Collection Meth... FHIRSpecimenCollectionMethod ?? » 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 SNOMEDCTBodyStructures ?? » Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection fastingStatus[x] : Type [0..1] « CodeableConcept | Duration ; Codes describing the fasting status of the patient. (Strength=Extensible) v2.0916 + » 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 specimen. (Strength=Example) 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 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 container. (Strength=Example) v2 Additive/Preservative v2.0371 ?? » 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><!-- 0..1 CodeableConcept Kind of material that forms the specimen --></type>
 <</subject>

 <subject><!-- 0..1 Reference(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 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>

 <request><!-- 0..* Reference(ServiceRequest) Why the specimen was collected --></request>

 <collection>  <!-- 0..1 Collection details -->
  <</collector>

  <collector><!-- 0..1 Reference(Practitioner|PractitionerRole) 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><!-- 0..1 CodeableConcept Anatomical collection site --></bodySite>
  <fastingStatus[x]><!-- 0..1 CodeableConcept|Duration Whether or how long patient abstained from food and/or drink --></fastingStatus[x]>

 </collection>
 <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>
 <condition><!-- 0..* CodeableConcept State of the specimen --></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
  "

  "subject" : { Reference(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 or a device

  "receivedTime" : "<dateTime>", // The time when specimen was received for processing
  "parent" : [{ Reference(Specimen) }], // Specimen from which this specimen originated
  "

  "request" : [{ Reference(ServiceRequest) }], // Why the specimen was collected

  "collection" : { // Collection details
    "

    "collector" : { Reference(Practitioner|PractitionerRole) }, // 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
    "

    "bodySite" : { CodeableConcept }, // 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
    "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) }
  }],
  "condition" : [{ CodeableConcept }], // State of the specimen

  "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:Specimen.subject [ Reference(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 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:

  fhir:Specimen.request [ Reference(ServiceRequest) ], ... ; # 0..* Why the specimen was collected

  fhir:Specimen.collection [ # 0..1 Collection details
    fhir:

    fhir:Specimen.collection.collector [ Reference(Practitioner|PractitionerRole) ]; # 0..1 Who collected the specimen

    # Specimen.collection.collected[x] : 0..1 Collection time. One of these 2
      fhir:Specimen.collection.collectedDateTime [ dateTime ]
      fhir:Specimen.collection.collectedPeriod [ Period ]
    fhir:Specimen.collection.duration [ Duration ]; # 0..1 How long it took to collect specimen

    fhir:Specimen.collection.quantity [ Quantity(SimpleQuantity) ]; # 0..1 The quantity of specimen collected
    fhir:Specimen.collection.method [ CodeableConcept ]; # 0..1 Technique used to perform collection
    fhir:Specimen.collection.bodySite [ CodeableConcept ]; # 0..1 Anatomical collection site
    # Specimen.collection.fastingStatus[x] : 0..1 Whether or how long patient abstained from food and/or drink. One of these 2
      fhir:Specimen.collection.fastingStatusCodeableConcept [ CodeableConcept ]
      fhir:Specimen.collection.fastingStatusDuration [ Duration ]

  ];
  fhir:Specimen.processing [ # 0..* Processing and processing step details
    fhir:Specimen.processing.description [ string ]; # 0..1 Textual description of procedure
    fhir:Specimen.processing.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.condition [ CodeableConcept ], ... ; # 0..* State of the specimen

  fhir:Specimen.note [ Annotation ], ... ; # 0..* Comments
]

Changes since DSTU2 R3

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 Specimen.status
  • deleted Change value set from http://hl7.org/fhir/ValueSet/specimen-status|4.0.0 to http://hl7.org/fhir/ValueSet/specimen-status|4.1.0

See the Full Difference for further information

This analysis is available as XML or JSON .

See R2 <--> R3 <--> R4 Conversion Maps (status = 6 4 tests that all execute ok. All tests pass round-trip testing and 1 2 r3 resources are invalid (1 (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 )
. . . type Σ 0..1 CodeableConcept Kind of material that forms the specimen
v2 Specimen Type ( Example )
. . . subject Σ 1..1 0..1 Reference ( Patient | Group | Device | Substance | Location ) Where the specimen came from. This may be from the patient(s) or patient(s), from a location (e.g., the environment source of an environmental sample), or a sampling of a substance or a device
. . . receivedTime Σ 0..1 dateTime The time when specimen was received for processing
. . . parent 0..* Reference ( Specimen ) Specimen from which this specimen originated
. . . request 0..* Reference ( ProcedureRequest ServiceRequest ) Why the specimen was collected
. . . collection 0..1 BackboneElement Collection details
. . . . collector Σ 0..1 Reference ( Practitioner | PractitionerRole ) 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 )
. . . . bodySite 0..1 CodeableConcept Anatomical collection site
SNOMED CT Body Structures ( Example )
. . . . fastingStatus[x] Σ 0..1 Whether or how long patient abstained from food and/or drink
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 0..1 CodeableConcept Indicates the treatment step applied to the specimen
SpecimenProcessingProcedure Specimen processing procedure ( 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 Specimen container ( 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 Additive ( Example )
. . . . . additiveCodeableConcept CodeableConcept
. . . . . additiveReference Reference ( Substance )
. . . condition Σ 0..* CodeableConcept State of the specimen
v2 Specimen Condition ( Extensible )
. . . 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 v2.0487 ?? » Where the specimen came from. This may be from the patient(s) or patient(s), from a location (e.g., the environment source of an environmental sample), or a sampling of a substance or a device subject : Reference [1..1] [0..1] « Patient | Group | Device | Substance | Location » Time when specimen was received 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 test or procedure service request that required a specimen to be collected request : Reference [0..*] ProcedureRequest « ServiceRequest » 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) v2.0493 + » 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..*] Collection Person who collected the specimen collector : Reference [0..1] « Practitioner | PractitionerRole » Time when specimen was collected from subject - the physiologically relevant time collected[x] : Type [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 that is used to perform the procedure procedure. (Strength=Example) FHIR Specimen Collection Meth... FHIRSpecimenCollectionMethod ?? » 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 SNOMEDCTBodyStructures ?? » Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection fastingStatus[x] : Type [0..1] « CodeableConcept | Duration ; Codes describing the fasting status of the patient. (Strength=Extensible) v2.0916 + » 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 specimen. (Strength=Example) 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 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 container. (Strength=Example) v2 Additive/Preservative v2.0371 ?? » 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><!-- 0..1 CodeableConcept Kind of material that forms the specimen --></type>
 <</subject>

 <subject><!-- 0..1 Reference(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 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>

 <request><!-- 0..* Reference(ServiceRequest) Why the specimen was collected --></request>

 <collection>  <!-- 0..1 Collection details -->
  <</collector>

  <collector><!-- 0..1 Reference(Practitioner|PractitionerRole) 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><!-- 0..1 CodeableConcept Anatomical collection site --></bodySite>
  <fastingStatus[x]><!-- 0..1 CodeableConcept|Duration Whether or how long patient abstained from food and/or drink --></fastingStatus[x]>

 </collection>
 <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>
 <condition><!-- 0..* CodeableConcept State of the specimen --></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
  "

  "subject" : { Reference(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 or a device

  "receivedTime" : "<dateTime>", // The time when specimen was received for processing
  "parent" : [{ Reference(Specimen) }], // Specimen from which this specimen originated
  "

  "request" : [{ Reference(ServiceRequest) }], // Why the specimen was collected

  "collection" : { // Collection details
    "

    "collector" : { Reference(Practitioner|PractitionerRole) }, // 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
    "

    "bodySite" : { CodeableConcept }, // 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
    "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) }
  }],
  "condition" : [{ CodeableConcept }], // State of the specimen

  "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:Specimen.subject [ Reference(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 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:

  fhir:Specimen.request [ Reference(ServiceRequest) ], ... ; # 0..* Why the specimen was collected

  fhir:Specimen.collection [ # 0..1 Collection details
    fhir:

    fhir:Specimen.collection.collector [ Reference(Practitioner|PractitionerRole) ]; # 0..1 Who collected the specimen

    # Specimen.collection.collected[x] : 0..1 Collection time. One of these 2
      fhir:Specimen.collection.collectedDateTime [ dateTime ]
      fhir:Specimen.collection.collectedPeriod [ Period ]
    fhir:Specimen.collection.duration [ Duration ]; # 0..1 How long it took to collect specimen

    fhir:Specimen.collection.quantity [ Quantity(SimpleQuantity) ]; # 0..1 The quantity of specimen collected
    fhir:Specimen.collection.method [ CodeableConcept ]; # 0..1 Technique used to perform collection
    fhir:Specimen.collection.bodySite [ CodeableConcept ]; # 0..1 Anatomical collection site
    # Specimen.collection.fastingStatus[x] : 0..1 Whether or how long patient abstained from food and/or drink. One of these 2
      fhir:Specimen.collection.fastingStatusCodeableConcept [ CodeableConcept ]
      fhir:Specimen.collection.fastingStatusDuration [ Duration ]

  ];
  fhir:Specimen.processing [ # 0..* Processing and processing step details
    fhir:Specimen.processing.description [ string ]; # 0..1 Textual description of procedure
    fhir:Specimen.processing.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.condition [ CodeableConcept ], ... ; # 0..* State of the specimen

  fhir:Specimen.note [ Annotation ], ... ; # 0..* Comments
]

Changes since DSTU2 Release 3

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 Specimen.status
  • deleted Change value set from http://hl7.org/fhir/ValueSet/specimen-status|4.0.0 to http://hl7.org/fhir/ValueSet/specimen-status|4.1.0

See the Full Difference for further information

This analysis is available as XML or JSON .

See R2 <--> R3 <--> R4 Conversion Maps (status = 6 4 tests that all execute ok. All tests pass round-trip testing and 1 2 r3 resources are invalid (1 (0 errors). ). )

 

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

10.6.3.1 10.7.4.1 Terminology Bindings

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 v2.0487
Specimen.collection.method The technique that is used to perform the procedure procedure. Example FHIR Specimen Collection Method FHIRSpecimenCollectionMethod
Specimen.collection.bodySite Codes describing anatomical locations. May include laterality. Example SNOMED CT Body Structures SNOMEDCTBodyStructures
Specimen.collection.fastingStatus[x] Codes describing the fasting status of the patient. Extensible v2.0916
Specimen.processing.procedure Type indicating the technique used to process the specimen specimen. Example SpecimenProcessingProcedure
Specimen.container.type Type of specimen container container. Example SpecimenContainer
Specimen.container.additive[x] Substance added to specimen container container. Example v2 Additive/Preservative v2.0371
Specimen.condition Codes describing the state of the specimen. Extensible v2.0493

10.6.4 10.7.5 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 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
collector reference Who collected the specimen Specimen.collection.collector
( Practitioner , PractitionerRole )
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 Specimen.subject.where(resolve() is Patient)
( Patient )
status token available | unavailable | unsatisfactory | entered-in-error Specimen.status
subject reference The subject of the specimen Specimen.subject
( Group , Device , Patient , Substance , Location )
type token The specimen type Specimen.type