Release 4B Snapshot #1
DiagnosticsThis page is part of the FHIR Specification v4.3.0-snapshot1: R4B Snapshot to support the Jan 2022 Connectathon. About the R4B version of FHIR. The current officially released version is 4.3.0. For a full list of available versions, see the Directory of published versions 
. Page versions: R5 R4B R4 R3 R2
| Orders and Observations Work Group | Maturity Level: 2 | Trial Use | Security Category: Patient | Compartments: Device, Patient, Practitioner |
A sample to be used for analysis.
Any material sample:
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.
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.
This resource is referenced by DiagnosticReport, ImagingStudy, Media, MolecularSequence, Observation, ServiceRequest and itself.
This resource does not implement any patterns.
Structure
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  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 hl7VS-specimenType (Example) |
 subject | Σ | 0..1 | Reference(Patient | Group | Device | Substance | Location) | 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 | 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(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 hl7VS-relevantClincialInformation (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 (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 hl7VS-additivePreservative (Example) | ||
| additiveCodeableConcept | CodeableConcept | |||
| additiveReference | Reference(Substance) | |||
| condition | Σ | 0..* | CodeableConcept | State of the specimen hl7VS-specimenCondition (Extensible) |
| note | 0..* | Annotation | Comments | |
| Documentation for this format | ||||
UML Diagram (Legend)
XML Template
<Specimen xmlns="http://hl7.org/fhir"><!-- 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
JSON Template
{
"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/> .
Changes since R3
| Specimen | |
| Specimen.status |
|
See the Full Difference for further information
This analysis is available as XML or JSON.
See R3 <--> R4 Conversion Maps (status = 4 tests that all execute ok. All tests pass round-trip testing and 2 r3 resources are invalid (0 errors).)
Structure
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| 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 hl7VS-specimenType (Example) |
| subject | Σ | 0..1 | Reference(Patient | Group | Device | Substance | Location) | 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 | 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(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 hl7VS-relevantClincialInformation (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 (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 hl7VS-additivePreservative (Example) | ||
| additiveCodeableConcept | CodeableConcept | |||
| additiveReference | Reference(Substance) | |||
| condition | Σ | 0..* | CodeableConcept | State of the specimen hl7VS-specimenCondition (Extensible) |
| note | 0..* | Annotation | Comments | |
| Documentation for this format | ||||
XML Template
<Specimen xmlns="http://hl7.org/fhir">
JSON Template
{
"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/> .
Changes since Release 3
| Specimen | |
| Specimen.status |
|
See the Full Difference for further information
This analysis is available as XML or JSON.
See R3 <--> R4 Conversion Maps (status = 4 tests that all execute ok. All tests pass round-trip testing and 2 r3 resources are invalid (0 errors).)
See the Profiles & Extensions and the alternate definitions: Master Definition XML + JSON, XML Schema/Schematron + JSON Schema, ShEx (for Turtle) + see the extensions & the dependency analysis
| Path | Definition | Type | Reference |
|---|---|---|---|
| Specimen.status | Required | SpecimenStatus | |
| Specimen.type | Example | Hl7VSSpecimenType | |
| Specimen.collection.method | Example | FHIRSpecimenCollectionMethod | |
| Specimen.collection.bodySite | Example | SNOMEDCTBodyStructures | |
| Specimen.collection.fastingStatus[x] | Extensible | Hl7VSRelevantClincialInformation | |
| Specimen.processing.procedure | Example | SpecimenProcessingProcedure | |
| Specimen.container.type | Example | SpecimenContainer | |
| Specimen.container.additive[x] | Example | Hl7VSAdditivePreservative | |
| Specimen.condition | Extensible | Hl7VSSpecimenCondition |
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.where(resolve() is Patient) (Group, Device, Patient, Substance, Location) | |
| 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 |
FHIR ®© HL7.org 2011+. FHIR R4B Ballot #1 hl7.fhir.core#4.3.0-snapshot1 generated on Mon, Dec 20, 2021 14:15+1100.
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