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4.19 Resource Specimen - Content

Sample for analysis.

4.19.1 Scope and Usage

Any material sample:

Biospecimen can contain one or more components including but not limited to cellular molecules, cells, tissues, organs, body fluids, embryos, and body excretory products (source: NCIt, 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.

4.19.2 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.

4.19.3 Resource Content

Specimen (Resource)Id for specimenidentifier : Identifier 0..*Kind of material that forms the specimentype : CodeableConcept 0..1 <<The type of the specimen.SpecimenType>>Where the specimen came from. This may be the patient(s) or from the environment or a devicesubject : Resource(Patient|Group|Device|Substance) 1..1The identifier assigned by the lab when accessioning specimen(s). This is not necessarily the same as the specimen identifier, depending on local lab proceduresaccessionIdentifier : Identifier 0..1Time when specimen was received for processing or testingreceivedTime : dateTime 0..1SourceWhether this relationship is to a parent or to a childrelationship : code 1..1 <<Type indicating if this is a parent or child relationshipHierarchicalRelationshipType>>The specimen resource that is the target of this relationshiptarget : Resource(Specimen) 0..*CollectionPerson who collected the specimencollector : Resource(Practitioner) 0..1To communicate any details or issues encountered during the specimen collection procedurecomment : string 0..*Time when specimen was collected from subject - the physiologically relevant timecollected[x] : dateTime|Period 0..1The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology samplequantity : Quantity 0..1A coded value specifying the technique that is used to perform the proceduremethod : CodeableConcept 0..1 <<The technique that is used to perform the procedureSpecimenCollectionMethod>>Anatomical location from which the specimen should be collected (if subject is a patient). This element is not used for environmental specimenssourceSite : CodeableConcept 0..1 <<Codes describing anatomical locations. May include lateralityBodySite>>TreatmentTextual description of proceduredescription : string 0..1A coded value specifying the procedure used to process the specimenprocedure : CodeableConcept 0..1 <<Type indicating the technique used to process the specimenSpecimenTreatmentProcedure>>Material used in the processing stepadditive : Resource(Substance) 0..*ContainerId 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 circumstancesidentifier : Identifier 0..*Textual description of the containerdescription : string 0..1The type of container associated with the specimen (e.g. slide, aliquot, etc)type : CodeableConcept 0..1 <<Type of specimen containerSpecimenContainerType>>The capacity (volume or other measure) the container may containcapacity : Quantity 0..1The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen typespecimenQuantity : Quantity 0..1Additive associated with the containeradditive : Resource(Substance) 0..1Parent specimen from which the focal specimen was a componentsource0..*Details concerning the specimen collectioncollection1..1Details concerning treatment and processing steps for the specimentreatment0..*The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed herecontainer0..*

This resource is referenced by DiagnosticOrder, DiagnosticReport, Media and Observation

<Specimen xmlns="http://hl7.org/fhir"> doco
 <!-- from Resource: extension, modifierExtension, language, text, and contained -->
 <identifier><!-- 0..* Identifier External Identifier --></identifier>
 <type><!-- 0..1 CodeableConcept Kind of material that forms the specimen --></type>
 <source>  <!-- 0..* Parent of specimen -->
  <relationship value="[code]"/><!-- 1..1 parent | child -->
  <target><!-- 0..* Resource(Specimen) The subject of the relationship --></target>
 </source>
 <subject><!-- 1..1 Resource(Patient|Group|Device|Substance) 
     Where the specimen came from. This may be the patient(s) or from the environment or  a device --></subject>
 <accessionIdentifier><!-- 0..1 Identifier Identifier assigned by the lab --></accessionIdentifier>
 <receivedTime value="[dateTime]"/><!-- 0..1 The time when specimen was received for processing -->
 <collection>  <!-- 1..1 Collection details -->
  <collector><!-- 0..1 Resource(Practitioner) Who collected the specimen --></collector>
  <comment value="[string]"/><!-- 0..* Collector comments -->
  <collected[x]><!-- 0..1 dateTime|Period Collection time --></collected[x]>
  <quantity><!-- 0..1 Quantity The quantity of specimen collected --></quantity>
  <method><!-- 0..1 CodeableConcept Technique used to perform collection --></method>
  <sourceSite><!-- 0..1 CodeableConcept Anatomical collection site --></sourceSite>
 </collection>
 <treatment>  <!-- 0..* Treatment and processing step details -->
  <description value="[string]"/><!-- 0..1 Textual description of procedure -->
  <procedure><!-- 0..1 CodeableConcept Indicates the treatment or processing step  applied to the specimen --></procedure>
  <additive><!-- 0..* Resource(Substance) Material used in the processing step --></additive>
 </treatment>
 <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 Container volume or size --></capacity>
  <specimenQuantity><!-- 0..1 Quantity Quantity of specimen within container --></specimenQuantity>
  <additive><!-- 0..1 Resource(Substance) Additive associated with container --></additive>
 </container>
</Specimen>

Alternate definitions: Schema/Schematron, Resource Profile

4.19.3.1 Terminology Bindings

PathDefinitionTypeReference
Specimen.type The type of the specimen.Examplehttp://hl7.org/fhir/v2/vs/0487
Specimen.source.relationship Type indicating if this is a parent or child relationshipFixedhttp://hl7.org/fhir/hierarchical-relationship-type
Specimen.collection.method The technique that is used to perform the procedureExamplehttp://hl7.org/fhir/vs/specimen-collection-method
Specimen.collection.sourceSite Codes describing anatomical locations. May include lateralityExamplehttp://hl7.org/fhir/vs/body-site
Specimen.treatment.procedure Type indicating the technique used to process the specimenExamplehttp://hl7.org/fhir/vs/specimen-treatment-procedure
Specimen.container.type Type of specimen containerExamplehttp://hl7.org/fhir/vs/specimen-container-type

4.19.4 Search Parameters

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

NameTypeDescriptionPaths
_idtokenThe logical resource id associated with the resource (must be supported by all servers)
_languagetokenThe language of the resource
subjectreferenceThe subject of the specimenSpecimen.subject
(Device, Patient, Substance, Group)
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