type: resource-definitionsresource: Specimen

Specimen Definitions

Specimen

Sample for analysis

Definition: A sample to be used for analysis.

Cardinality: 0..*

Constraints: spm-1 | error | Specimen.collection.collector SHALL only be present if Specimen.collection.procedure is not present | collection.collector.empty() or collection.procedure.empty()

Mappings: rim=Role[classCode=SPEC]; w5=clinical.diagnostics

Specimen.identifier

Primary specimen identifier

Definition: Identifiers used for specimen identification. These could include but are not limited to identifiers generated upon collection, accessioning, or other reasons for labeling a specimen.

Comments: These are business identifiers, not Specimen.id - the resource identifier. More information in this (see discussion). For accession identifiers, the Accession Identifier code, ACSN, should be used in the Identifier.type.

Cardinality: 0..*

Type: Identifier

Summary: true

Mappings: w5=FiveWs.identifier; v2=SPM-2; rim=.id

Specimen.status

available | unavailable | unsatisfactory | entered-in-error

Definition: The availability of the specimen.

Comments: This element is labeled as a modifier because the status contains codes that mark the resource as not currently valid.

Cardinality: 0..1

Type: code

Binding: required:specimen-status

Summary: true

Is Modifier: true (Reason: This element is labelled as a modifier because it is a status element that contains status entered-in-error which means that the resource should not be treated as valid)

Mappings: w5=FiveWs.status; v2=SPM-20; rim=status

Specimen.type

Kind of material that forms the specimen

Definition: The kind of material that forms the specimen.

Comments: The type can change the way that a specimen is handled and drives what kind of analyses can properly be performed on the specimen. It is frequently used in diagnostic work flow decision making systems.

Cardinality: 0..1

Type: CodeableConcept

Binding: example:v2-0487

Summary: true

Mappings: w5=FiveWs.what[x]; v2=SPM-4 and possibly SPM-5; rim=.code

Specimen.subject

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

Definition: 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.

Requirements: Must know the subject context.

Cardinality: 0..1

Type: Reference(Patient, Group, Device, BiologicallyDerivedProduct, Substance, Location, NutritionProduct)

Summary: true

Mappings: w5=FiveWs.subject; rim=.scoper or .scoper.playsRole

Specimen.receivedTime

The time when specimen is received by the testing laboratory

Definition: Time when specimen is received by the testing laboratory for processing or testing.

Cardinality: 0..1

Type: dateTime

Summary: true

Mappings: w5=FiveWs.done[x]; v2=SPM-18; rim=.participation[typeCode=SBJ].act[code=SPCREC, moodCode=EVN].effectiveTime

Specimen.parent

Specimen from which this specimen originated

Definition: Reference to the parent (source) specimen which is used when the specimen was either derived from or a component of another specimen.

Comments: The parent specimen could be the source from which the current specimen is derived by some processing step (e.g. an aliquot or isolate or extracted nucleic acids from clinical samples) or one of many specimens that were combined to create a pooled sample.

Cardinality: 0..*

Type: Reference(Specimen)

Mappings: rim=.scoper (if parent) .player.scopesRole[classCode=SPEC].player (if child)

Specimen.request

Why the specimen was collected

Definition: Details concerning a service request that required a specimen to be collected.

Comments: The request may be explicit or implied such with a ServiceRequest that requires a blood draw.

Cardinality: 0..*

Type: Reference(ServiceRequest)

Mappings: w5=FiveWs.why[x]; v2=ORC? OBR-2/3?; rim=outboundRelationship[typeCode=FLFS].target

Specimen.combined

grouped | pooled

Definition: This element signifies if the specimen is part of a group or pooled.

Cardinality: 0..1

Type: code

Binding: required:specimen-combined

Summary: true

Specimen.role

The role the specimen serves

Definition: The role or reason for the specimen in the testing workflow.

Cardinality: 0..*

Type: CodeableConcept

Binding: preferred:specimen-role

Mappings: v2=SPM-10

Specimen.feature

The physical feature of a specimen

Definition: A physical feature or landmark on a specimen, highlighted for context by the collector of the specimen (e.g. surgeon), that identifies the type of feature as well as its meaning (e.g. the red ink indicating the resection margin of the right lobe of the excised prostate tissue or wire loop at radiologically suspected tumor location).

Cardinality: 0..*

Type: BackboneElement

Mappings: rim=.player.scopingRole[classCode=FEAT].scoper

Specimen.feature.type

Highlighted feature

Definition: The landmark or feature being highlighted.

Cardinality: 1..1

Type: CodeableConcept

Binding: example:body-site

Mappings: w5=FiveWs.what[x]; rim=.code

Specimen.feature.description

Information about the feature

Definition: Description of the feature of the specimen.

Cardinality: 1..1

Type: string

Mappings: rim=.text

Specimen.collection

Collection details

Definition: Details concerning the specimen collection.

Cardinality: 0..1

Type: BackboneElement

Mappings: v2=SPM-14; rim=.participation[typeCode=SBJ].act[classCode=SPECCOLLECT, moodCode=EVN]

Specimen.collection.collector

Who collected the specimen

Definition: Person who collected the specimen.

Conditions: spm-1

Cardinality: 0..1

Type: Reference(Organization, Practitioner, PractitionerRole, Patient, RelatedPerson)

Summary: true

Mappings: w5=FiveWs.actor; v2=PRT; rim=.participation[typeCode=PFM].role

Specimen.collection.collected[x]

Collection time

Definition: Time when specimen was collected from subject - the physiologically relevant time.

Cardinality: 0..1

Type: dateTime, Period

Summary: true

Mappings: w5=FiveWs.init; v2=SPM-17; rim=.effectiveTime

Specimen.collection.duration

How long it took to collect specimen

Definition: The span of time over which the collection of a specimen occurred.

Cardinality: 0..1

Type: Duration

Summary: true

Mappings: w5=FiveWs.init

Specimen.collection.quantity

The quantity of specimen collected

Definition: The quantity of specimen collected; for instance the volume of a blood sample, or the physical measurement of an anatomic pathology sample.

Cardinality: 0..1

Type: Quantity(SimpleQuantity)

Mappings: v2=SPM-12; rim=.participation[typeCode=SBJ].role[classCode=SPEC].player.quantity

Specimen.collection.method

Technique used to perform collection

Definition: A coded value specifying the technique that is used to perform the procedure.

Cardinality: 0..1

Type: CodeableConcept

Binding: example:specimen-collection-method

Mappings: v2=SPM-7; rim=.methodCode

Specimen.collection.device[x]

Device used to perform collection

Definition: A coded value specifying the device that is used to perform the procedure.

Cardinality: 0..1

Type: CodeableConcept, Reference(Device), canonical

Binding: example:specimen-container-type

Mappings: v2=SPM-14; rim=participation[typeCode=DEV]

Specimen.collection.procedure

The procedure that collects the specimen

Definition: The procedure event during which the specimen was collected (e.g. the surgery leading to the collection of a pathology sample).

Conditions: spm-1

Cardinality: 0..1

Type: Reference(Procedure)

Specimen.collection.bodySite

Anatomical collection site

Definition: 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.

Comments: Reasons for using BodyStructure reference include: 1.) Need to identify a specific site instance (e.g. a specific mole), 2.) a single pre-coordinated coded concept for the body site does not exist, 3.) a desire to represent bodySite using multiple attributes (e.g. modifiers).

Cardinality: 0..1

Type: CodeableReference

Binding: example:body-site

Mappings: v2=SPM-8 and SPM-9; rim=.targetSiteCode

Specimen.collection.fastingStatus[x]

Whether or how long patient abstained from food and/or drink

Definition: Abstinence or reduction from some or all food, drink, or both, for a period of time prior to sample collection.

Comments: Representing fasting status using this element is preferred to representing it with an observation using a 'pre-coordinated code' such as LOINC 2005-7 (Calcium [Moles/time] in 2 hour Urine --12 hours fasting), or using a component observation such asObservation.component code` = LOINC 49541-6 (Fasting status - Reported).

Requirements: Many diagnostic tests require fasting to facilitate accurate interpretation.

Cardinality: 0..1

Type: CodeableConcept, Duration

Binding: extensible:v2-0916

Summary: true

Mappings: v2=OBR-

Specimen.processing

Processing and processing step details

Definition: Details concerning processing and processing steps for the specimen.

Cardinality: 0..*

Type: BackboneElement

Mappings: rim=.participation[typeCode=SBJ].act[code=SPCTRT, moodCode=EVN]

Specimen.processing.description

Textual description of procedure

Definition: Textual description of procedure.

Cardinality: 0..1

Type: string

Mappings: rim=.text

Specimen.processing.method

Indicates the treatment step applied to the specimen

Definition: A coded value specifying the method used to process the specimen.

Cardinality: 0..1

Type: CodeableConcept

Binding: example:specimen-processing-method

Mappings: rim=.code

Specimen.processing.performer

Entity processing specimen

Definition: The performer of the processing of the specimen.

Cardinality: 0..1

Type: Reference(Practitioner, PractitionerRole, Patient, RelatedPerson)

Summary: true

Mappings: w5=FiveWs.actor; v2=PRT; rim=.participation[typeCode=PFM].role

Specimen.processing.device[x]

Device used to process the specimen

Definition: The device used in the processing of the specimen.

Cardinality: 0..1

Type: CodeableConcept, Reference(Device), canonical

Binding: example:processingdevice-code

Mappings: rim=participation[typeCode=DEV]

Specimen.processing.additive

Material used in the processing step

Definition: Material used in the processing step.

Cardinality: 0..*

Type: CodeableReference

Mappings: v2=SPM-6; rim=.participation[typeCode=CSM].role[classCode=ADTV].code

Specimen.processing.time[x]

Date and time of specimen processing

Definition: 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.

Cardinality: 0..1

Type: dateTime, Period, Duration

Mappings: rim=.effectiveTime

Specimen.container

Direct container of specimen (tube/slide, etc.)

Definition: The container holding the specimen. The recursive nature of containers; i.e. blood in tube in tray in rack is not addressed here.

Cardinality: 0..*

Type: BackboneElement

Mappings: rim=.player.scopingRole[classCode=CONT].scoper

Specimen.container.device[x]

Device resource for the container

Definition: The device resource for the the container holding the specimen. If the container is in a holder then the referenced device will point to a parent device.

Cardinality: 1..1

Type: CodeableConcept, Reference(Device), canonical

Binding: example:containerdevice-code

Mappings: rim=participation[typeCode=DEV]

Specimen.container.specimenQuantity

Quantity of specimen within container

Definition: The quantity of specimen in the container; may be volume, dimensions, or other appropriate measurements, depending on the specimen type.

Cardinality: 0..1

Type: Quantity(SimpleQuantity)

Mappings: v2=SAC-23 (value) SAC-24 (units; rim=.playedRole[classCode=CONT].quantity

Specimen.condition

State of the specimen

Definition: A mode or state of being that describes the nature of the specimen.

Comments: Specimen condition is an observation made about the specimen. It's a point-in-time assessment. It can be used to assess its quality or appropriateness for a specific test.

Requirements: The specimen condition can be used to assess its quality or appropriateness for a specific test.

Cardinality: 0..*

Type: CodeableConcept

Binding: example:v2-0493

Summary: true

Mappings: v2=SPM-24

Specimen.note

Comments

Definition: To communicate any details or issues about the specimen or during the specimen collection. (for example: broken vial, sent with patient, frozen).

Cardinality: 0..*

Type: Annotation

Mappings: v2=OBX; rim=.inboundRelationship[typeCode=SUBJ].source[classCode=OBS, moodCode=EVN, code="annotation"].value