Snapshot 3: Connectathon 32 Base
DiagnosticsThis page is part of the FHIR Specification (v5.0.0-snapshot3: R5 Snapshot #3, to support Connectathon 32). The current version which supercedes this version is 5.0.0. 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.
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 | BiologicallyDerivedProduct | 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, 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 SpecimenCombined (Required) |
| role | 0..* | CodeableConcept | The role the specimen serves SpecimenRole (Preferred) | |
  feature | 0..* | BackboneElement | The physical feature of a specimen | |
 type | 1..1 | CodeableConcept | Highlighted feature SNOMED CT Body Structures (Example) | |
 description | 1..1 | string | Information about the feature | |
| collection | 0..1 | BackboneElement | Collection details | |
| collector | Σ | 0..1 | Reference(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 FHIR Specimen Collection Method (Example) | |
| device | 0..1 | CodeableReference(Device) | Device used to perform collection SpecimenCollectionDevice (Example) | |
| procedure | 0..1 | Reference(Procedure) | The procedure that collects the specimen | |
| bodySite | 0..1 | CodeableReference(BodyStructure) | 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 | |
| method | 0..1 | CodeableConcept | Indicates the treatment step applied to the specimen SpecimenProcessingMethod (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.) | |
| device | 1..1 | Reference(Device) | Device resource for the container | |
| location | 0..1 | Reference(Location) | Where the container is | |
| specimenQuantity | 0..1 | SimpleQuantity | Quantity of specimen within container | |
| condition | Σ | 0..* | CodeableConcept | State of the specimen hl7VS-specimenCondition (Extensible) |
| note | 0..* | Annotation | Comments | |
| Documentation for this format | ||||
See the Extensions for this resource
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(BiologicallyDerivedProduct|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, a biologically-derived product, or a device
"receivedTime" : "<dateTime>", // The time when specimen is received by the testing laboratory
"parent" : [{ Reference(Specimen) }], // Specimen from which this specimen originated
"request" : [{ Reference(ServiceRequest) }], // Why the specimen was collected
"combined" : "<code>", // grouped | pooled
"role" : [{ CodeableConcept }], // The role the specimen serves
"feature" : [{ // The physical feature of a specimen
"type" : { CodeableConcept }, // R! Highlighted feature
"description" : "<string>" // R! Information about the feature
}],
"collection" : { // Collection details
"collector" : { Reference(Patient|Practitioner|PractitionerRole|
RelatedPerson) }, // 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
"device" : { CodeableReference(Device) }, // Device used to perform collection
"procedure" : { Reference(Procedure) }, // The procedure that collects the specimen
"bodySite" : { CodeableReference(BodyStructure) }, // 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
"method" : { 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.)
"device" : { Reference(Device) }, // R! Device resource for the container
"location" : { Reference(Location) }, // Where the container is
"specimenQuantity" : { Quantity(SimpleQuantity) } // Quantity of specimen within container
}],
"condition" : [{ CodeableConcept }], // State of the specimen
"note" : [{ Annotation }] // Comments
}
Turtle Template
@prefix fhir: <http://hl7.org/fhir/> .
Changes since R4
| Specimen | |
| Specimen.subject |
|
| Specimen.combined |
|
| Specimen.role |
|
| Specimen.feature |
|
| Specimen.feature.type |
|
| Specimen.feature.description |
|
| Specimen.collection.collector |
|
| Specimen.collection.device |
|
| Specimen.collection.procedure |
|
| Specimen.collection.bodySite |
|
| Specimen.processing.method |
|
| Specimen.container.device |
|
| Specimen.container.location |
|
| Specimen.processing.procedure |
|
| Specimen.container.identifier |
|
| Specimen.container.description |
|
| Specimen.container.type |
|
| Specimen.container.capacity |
|
| Specimen.container.additive[x] |
|
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 | BiologicallyDerivedProduct | 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, 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 SpecimenCombined (Required) |
| role | 0..* | CodeableConcept | The role the specimen serves SpecimenRole (Preferred) | |
| feature | 0..* | BackboneElement | The physical feature of a specimen | |
| type | 1..1 | CodeableConcept | Highlighted feature SNOMED CT Body Structures (Example) | |
| description | 1..1 | string | Information about the feature | |
| collection | 0..1 | BackboneElement | Collection details | |
| collector | Σ | 0..1 | Reference(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 FHIR Specimen Collection Method (Example) | |
| device | 0..1 | CodeableReference(Device) | Device used to perform collection SpecimenCollectionDevice (Example) | |
| procedure | 0..1 | Reference(Procedure) | The procedure that collects the specimen | |
| bodySite | 0..1 | CodeableReference(BodyStructure) | 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 | |
| method | 0..1 | CodeableConcept | Indicates the treatment step applied to the specimen SpecimenProcessingMethod (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.) | |
| device | 1..1 | Reference(Device) | Device resource for the container | |
| location | 0..1 | Reference(Location) | Where the container is | |
| specimenQuantity | 0..1 | SimpleQuantity | Quantity of specimen within container | |
| condition | Σ | 0..* | CodeableConcept | State of the specimen hl7VS-specimenCondition (Extensible) |
| note | 0..* | Annotation | Comments | |
| Documentation for this format | ||||
See the Extensions for this resource
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(BiologicallyDerivedProduct|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, a biologically-derived product, or a device
"receivedTime" : "<dateTime>", // The time when specimen is received by the testing laboratory
"parent" : [{ Reference(Specimen) }], // Specimen from which this specimen originated
"request" : [{ Reference(ServiceRequest) }], // Why the specimen was collected
"combined" : "<code>", // grouped | pooled
"role" : [{ CodeableConcept }], // The role the specimen serves
"feature" : [{ // The physical feature of a specimen
"type" : { CodeableConcept }, // R! Highlighted feature
"description" : "<string>" // R! Information about the feature
}],
"collection" : { // Collection details
"collector" : { Reference(Patient|Practitioner|PractitionerRole|
RelatedPerson) }, // 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
"device" : { CodeableReference(Device) }, // Device used to perform collection
"procedure" : { Reference(Procedure) }, // The procedure that collects the specimen
"bodySite" : { CodeableReference(BodyStructure) }, // 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
"method" : { 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.)
"device" : { Reference(Device) }, // R! Device resource for the container
"location" : { Reference(Location) }, // Where the container is
"specimenQuantity" : { Quantity(SimpleQuantity) } // Quantity of specimen within container
}],
"condition" : [{ CodeableConcept }], // State of the specimen
"note" : [{ Annotation }] // Comments
}
Turtle Template
@prefix fhir: <http://hl7.org/fhir/> .
Changes since Release 4
| Specimen | |
| Specimen.subject |
|
| Specimen.combined |
|
| Specimen.role |
|
| Specimen.feature |
|
| Specimen.feature.type |
|
| Specimen.feature.description |
|
| Specimen.collection.collector |
|
| Specimen.collection.device |
|
| Specimen.collection.procedure |
|
| Specimen.collection.bodySite |
|
| Specimen.processing.method |
|
| Specimen.container.device |
|
| Specimen.container.location |
|
| Specimen.processing.procedure |
|
| Specimen.container.identifier |
|
| Specimen.container.description |
|
| Specimen.container.type |
|
| Specimen.container.capacity |
|
| Specimen.container.additive[x] |
|
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).)
Additional definitions: Master Definition XML + JSON, XML Schema/Schematron + JSON Schema, ShEx (for Turtle) + see the extensions, the spreadsheet version & the dependency analysis
| Path | Definition | Type | Reference |
|---|---|---|---|
| Specimen.status | Codes providing the status/availability of a specimen. | Required | SpecimenStatus |
| Specimen.type | 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. | Example | Hl7VSSpecimenType (a valid code from specimenType ) |
| Specimen.combined | Codes providing the combined status of a specimen. | Required | SpecimenCombined |
| Specimen.role | Codes providing the role of a specimen. | Preferred | SpecimenRole |
| Specimen.feature.type | This value set includes all codes from SNOMED CT | Example | SNOMEDCTBodyStructures |
| Specimen.collection.method | This example value set defines a set of codes that can be used to indicate the method by which a specimen was collected. | Example | FHIRSpecimenCollectionMethod |
| Specimen.collection.device | Example | ?? | |
| Specimen.collection.bodySite | This value set includes all codes from SNOMED CT | Example | SNOMEDCTBodyStructures |
| Specimen.collection.fastingStatus[x] | 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. | Extensible | Hl7VSRelevantClincialInformation (a valid code from relevantClincialInformation ) |
| Specimen.processing.method | The technique that is used to perform the process or preserve the specimen. | Example | SpecimenProcessingMethod (a valid code from treatment ) |
| Specimen.condition | Concepts of modes or states of being that describe the nature of a specimen. Used in Version 2 messaging in the SPM segment. | Extensible | Hl7VSSpecimenCondition (a valid code from specimenCondition ) |
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 | reference | Reference to a resource (by instance) | Specimen.collection.bodySite.reference | |
| collected | date | The date the specimen was collected | Specimen.collection.collected.as(dateTime) | Specimen.collection.collected.as(Period) | |
| collector | reference | Who collected the specimen | Specimen.collection.collector (Practitioner, Patient, PractitionerRole, RelatedPerson) | |
| container-device | reference | The unique identifier associated with the specimen container | Specimen.container.device.where(resolve() is Device) (Device) | |
| 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) (Patient) | |
| 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, Device, Patient, Substance, Location) | |
| type | token | The specimen type | Specimen.type |
FHIR ®© HL7.org 2011+. FHIR R5 Snapshot 3, hl7.fhir.core#5.0.0-snapshot3 generated on Wed, Dec 14, 2022 07:17+1100.
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