This page is part of the Genetic Reporting Implementation Guide (v0.3.0: STU 1 Ballot 2) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
The official URL for this profile is:
http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen
Description of Profiles, Differentials, Snapshots and how the different presentations work.
This structure is derived from Specimen
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Specimen | I | 0..* | Specimen | |
  id | Σ | 0..1 | id | Logical id of this artifact |
 meta | Σ | 0..1 | Meta | Metadata about the resource |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred) | |
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |
 contained | 0..* | Resource | Contained, inline Resources | |
 extension | 0..* | Extension | Additional content defined by implementations | |
 modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| 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: SpecimenStatus (required) |
| type | Σ | 0..1 | CodeableConcept | Kind of material that forms the specimen Binding: v2 Specimen Type (example) |
 subject | SΣ | 1..1 | Reference(Patient | Group | 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 | I | 0..1 | BackboneElement | Collection details |
 id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| collector | Σ | 0..1 | Reference(Practitioner) | Who collected the specimen |
 collected[x] | Σ | 0..1 | dateTime, Period | Collection time |
| 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: FHIRSpecimenCollectionMethod (example) | |
| bodySite | 0..1 | CodeableConcept | Anatomical collection site Binding: SNOMEDCTBodyStructures (example) | |
 fastingStatus[x] | Σ | 0..1 | CodeableConcept, Duration | Whether or how long patient abstained from food and/or drink Binding: v2 Relevant Clincial Information (extensible) |
| processing | I | 0..* | BackboneElement | Processing and processing step details |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| description | 0..1 | string | Textual description of procedure | |
| procedure | 0..1 | CodeableConcept | Indicates the treatment step applied to the specimen Binding: SpecimenProcessingProcedure (example) | |
| additive | 0..* | Reference(Substance) | Material used in the processing step | |
| time[x] | 0..1 | dateTime, Period | Date and time of specimen processing | |
| container | I | 0..* | BackboneElement | Direct container of specimen (tube/slide, etc.) |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| 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 Binding: SpecimenContainerType (example) | |
| capacity | 0..1 | SimpleQuantity | Container volume or size | |
| specimenQuantity | 0..1 | SimpleQuantity | Quantity of specimen within container | |
| additive[x] | 0..1 | CodeableConcept, Reference(Substance) | Additive associated with container Binding: v2 Additive (example) | |
| condition | Σ | 0..* | CodeableConcept | State of the specimen Binding: v2 Specimen Condition (extensible) |
| note | 0..* | Annotation | Comments | |
| Documentation for this format | ||||
This structure is derived from Specimen
Differential View
This structure is derived from Specimen
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Specimen | I | 0..* | Specimen | |
| id | Σ | 0..1 | id | Logical id of this artifact |
| meta | Σ | 0..1 | Meta | Metadata about the resource |
| implicitRules | ?!Σ | 0..1 | uri | A set of rules under which this content was created |
| language | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred) | |
| text | 0..1 | Narrative | Text summary of the resource, for human interpretation | |
| contained | 0..* | Resource | Contained, inline Resources | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| modifierExtension | ?! | 0..* | Extension | Extensions that cannot be ignored |
| 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: SpecimenStatus (required) |
| type | Σ | 0..1 | CodeableConcept | Kind of material that forms the specimen Binding: v2 Specimen Type (example) |
| subject | SΣ | 1..1 | Reference(Patient | Group | 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 | I | 0..1 | BackboneElement | Collection details |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| collector | Σ | 0..1 | Reference(Practitioner) | Who collected the specimen |
| collected[x] | Σ | 0..1 | dateTime, Period | Collection time |
| 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: FHIRSpecimenCollectionMethod (example) | |
| bodySite | 0..1 | CodeableConcept | Anatomical collection site Binding: SNOMEDCTBodyStructures (example) | |
| fastingStatus[x] | Σ | 0..1 | CodeableConcept, Duration | Whether or how long patient abstained from food and/or drink Binding: v2 Relevant Clincial Information (extensible) |
| processing | I | 0..* | BackboneElement | Processing and processing step details |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| description | 0..1 | string | Textual description of procedure | |
| procedure | 0..1 | CodeableConcept | Indicates the treatment step applied to the specimen Binding: SpecimenProcessingProcedure (example) | |
| additive | 0..* | Reference(Substance) | Material used in the processing step | |
| time[x] | 0..1 | dateTime, Period | Date and time of specimen processing | |
| container | I | 0..* | BackboneElement | Direct container of specimen (tube/slide, etc.) |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | 0..* | Extension | Additional content defined by implementations | |
| modifierExtension | ?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| 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 Binding: SpecimenContainerType (example) | |
| capacity | 0..1 | SimpleQuantity | Container volume or size | |
| specimenQuantity | 0..1 | SimpleQuantity | Quantity of specimen within container | |
| additive[x] | 0..1 | CodeableConcept, Reference(Substance) | Additive associated with container Binding: v2 Additive (example) | |
| condition | Σ | 0..* | CodeableConcept | State of the specimen Binding: v2 Specimen Condition (extensible) |
| note | 0..* | Annotation | Comments | |
| Documentation for this format | ||||
Other representations of profile: Schematron
| Path | Name | Conformance | ValueSet |
| Specimen.language | Common Languages | preferred | CommonLanguages |
| Specimen.status | SpecimenStatus | required | SpecimenStatus |
| Specimen.type | v2 Specimen Type | example | v2.0487 |
| Specimen.collection.method | FHIR Specimen Collection Method | example | FHIRSpecimenCollectionMethod |
| Specimen.collection.bodySite | SNOMED CT Body Structures | example | SNOMEDCTBodyStructures |
| Specimen.collection.fastingStatus[x] | v2 Relevant Clincial Information | extensible | v2.0916 |
| Specimen.processing.procedure | Specimen processing procedure | example | SpecimenProcessingProcedure |
| Specimen.container.type | Specimen Container Type | example | SpecimenContainerType |
| Specimen.container.additive[x] | v2 Additive | example | v2.0371 |
| Specimen.condition | v2 Specimen Condition | extensible | v2.0493 |
| Id | Path | Details | Requirements |
| dom-2 | Specimen | If the resource is contained in another resource, it SHALL NOT contain nested Resources : contained.contained.empty() | |
| dom-4 | Specimen | If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated : contained.meta.versionId.empty() and contained.meta.lastUpdated.empty() | |
| dom-3 | Specimen | If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource : contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty() | |
| dom-6 | Specimen | A resource should have narrative for robust management : text.div.exists() | |
| dom-5 | Specimen | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| ele-1 | Specimen.collection | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.processing | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.container | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) |
Implementation Guide v0.3.0, based on FHIR v4.0.0. © 2017+ HL7 International Clinical Genomics Work Group. IG generated on Tue, Dec 4, 2018 11:36+1100.
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