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10.9 Resource Specimen - Content

Orders and Observations icon Work GroupMaturity Level: 3 Trial UseSecurity Category: Patient Compartments: Device, Group, Patient, Practitioner

A sample to be used for analysis.

10.9.1 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.

10.9.2 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.

10.9.3 References to this Resource

10.9.4 Resource Content

Structure

NameFlagsCard.TypeDescription & Constraintsdoco
.. Specimen TU DomainResource Sample for analysis
+ Rule: Specimen.collection.collector SHALL only be present if Specimen.collection.procedure is not present

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

... accessionIdentifier Σ 0..1 Identifier Identifier assigned by the lab
... status ?!Σ 0..1 code available | unavailable | unsatisfactory | entered-in-error
Binding: Specimen Status (Required)
... subject Σ 0..1 Reference(Patient | Group | Device | BiologicallyDerivedProduct | Substance | Location | NutritionProduct) 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 Σ 0..1 dateTime The time when specimen is received 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
Binding: Specimen Combined (Required)
... role 0..* CodeableConcept The role the specimen serves
Binding: Specimen Role (Preferred)

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

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

.... description 0..1 string Textual description of procedure
.... method 0..1 CodeableConcept Indicates the treatment step applied to the specimen
Binding: Specimen Processing Method (Example)
.... performer Σ 0..1 Reference(Practitioner | PractitionerRole | Patient | RelatedPerson) Entity processing specimen
.... device 0..1 Reference(Device) Device used to process the specimen
.... additive 0..* Reference(Substance) Material used in the processing step

.... time[x] 0..1 Date and time of specimen processing
..... timeDateTime dateTime
..... timePeriod Period
..... timeDuration Duration
... container 0..* BackboneElement Direct container of specimen (tube/slide, etc.)

.... device 1..1 Reference(Device) Device resource for the container
.... specimenQuantity 0..1 SimpleQuantity Quantity of specimen within container
... condition Σ 0..* CodeableConcept State of the specimen
Binding: hl7VS-specimenCondition icon (Extensible)

... note 0..* Annotation Comments


doco Documentation for this format icon

See the Extensions for this resource

 

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

10.9.4.1 Terminology Bindings

Path ValueSet Type Documentation
Specimen.status SpecimenStatus Required

Codes providing the status/availability of a specimen.
Specimen.type Hl7VSSpecimenType icon (a valid code from specimenType icon) Example

Concepts that describe the precise nature of an entity that may be used as the source material for an observation. This is one of two code systems that are used instead of table 0070 (code system xxxx) which conflated specimen types and specimen collection methods. Used in Version 2 messaging in the SPM segment.
Specimen.combined SpecimenCombined Required

Codes providing the combined status of a specimen.
Specimen.role SpecimenRole Preferred

Codes providing the role of a specimen.
Specimen.feature.type SNOMEDCTBodyStructures Example

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

This example value set defines a set of codes that can be used to indicate the method by which a specimen was collected.
Specimen.collection.device Example
Specimen.collection.bodySite SNOMEDCTBodyStructures Example

This value set includes all codes from SNOMED CT icon where concept is-a 442083009 (Anatomical or acquired body site (body structure)).
Specimen.collection.fastingStatus[x] Hl7VSRelevantClincialInformation icon (a valid code from relevantClincialInformation icon) Extensible

Value Set of codes that specify additional clinical information about the patient or specimen to report the supporting and/or suspected diagnosis and clinical findings on requests for interpreted diagnostic studies.
Specimen.processing.method SpecimenProcessingMethod Example

The technique that is used to perform the process or preserve the specimen. These are codes from SNOMED CT - provided as an exemplar value set.
Specimen.condition Hl7VSSpecimenCondition icon (a valid code from specimenCondition icon) Extensible

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

10.9.4.2 Constraints

UniqueKeyLevelLocationDescriptionExpression
img spm-1Rule (base)Specimen.collection.collector SHALL only be present if Specimen.collection.procedure is not presentcollection.collector.empty() or collection.procedure.empty()

10.9.5 Notes:

10.9.5.1 Specimen Grouping

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

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

10.9.5.2 Specimen Searching

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

10.9.6 Search Parameters

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

Name Type Description Expression In Common
accession token The accession number associated with the specimen Specimen.accessionIdentifier
bodysite reference Reference to a resource (by instance) Specimen.collection.bodySite.reference
collected date The date the specimen was collected Specimen.collection.collected.ofType(dateTime) | Specimen.collection.collected.ofType(Period)
collector reference Who collected the specimen Specimen.collection.collector
(Practitioner, Organization, Patient, PractitionerRole, RelatedPerson)
container-device reference The unique identifier associated with the specimen container Specimen.container.device.where(resolve() is Device)
(Device)
container-location reference The location of the specimen container Specimen.container.device.resolve().location
identifier token The unique identifier associated with the specimen Specimen.identifier 65 Resources
organization reference The organization where the specimen is located Specimen.container.device.resolve().owner
parent reference The parent of the specimen Specimen.parent
(Specimen)
patient reference The patient the specimen comes from Specimen.subject.where(resolve() is Patient)
(Patient)		 65 Resources
procedure reference The procedure that collected the specimen Specimen.collection.procedure
(Procedure)
status token available | unavailable | unsatisfactory | entered-in-error Specimen.status
subject reference The subject of the specimen Specimen.subject
(Group, BiologicallyDerivedProduct, NutritionProduct, Device, Patient, Substance, Location)
type token The specimen type Specimen.type 11 Resources