Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) 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 
| Defining URL: | http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/specimen |
| Version: | 1.1.0 |
| Name: | GenomicSpecimen |
| Title: | Genomics specimen |
| Status: | Active as of 2021-04-13T19:13:37+00:00 |
| Definition: | A sample to be used for analysis. |
| Publisher: | HL7 International Clinical Genomics Work Group |
| Source Resource: | XML / JSON / Turtle |
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
This structure is derived from Specimen
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Specimen | 0..* | Specimen | Sample for analysis | |
  subject | 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 | |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Specimen | 0..* | Specimen | Sample for analysis | |
  id | Σ | 0..1 | string | 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) Max Binding: AllLanguages: A human language. | |
| 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): Codes providing the status/availability of a specimen. |
| type | Σ | 0..1 | CodeableConcept | Kind of material that forms the specimen Binding: hl7VS-specimenType (example): The type of the specimen. |
| subject | Σ | 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 | 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 | 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 Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure. | |
| bodySite | 0..1 | CodeableConcept | Anatomical collection site Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | |
 fastingStatus[x] | Σ | 0..1 | Whether or how long patient abstained from food and/or drink Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient. | |
 fastingStatusCodeableConcept | CodeableConcept | |||
| fastingStatusDuration | Duration | |||
| processing | 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): Type indicating the technique 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 | |||
| container | 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): Type of specimen container. | |
| 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 Binding: hl7VS-additivePreservative (example): Substance added to specimen container. | ||
| additiveCodeableConcept | CodeableConcept | |||
| additiveReference | Reference(Substance) | |||
| condition | Σ | 0..* | CodeableConcept | State of the specimen Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen. |
| note | 0..* | Annotation | Comments | |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Specimen | 0..* | Specimen | Sample for analysis | |
| Documentation for this format | ||||
This structure is derived from Specimen
Differential View
This structure is derived from Specimen
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Specimen | 0..* | Specimen | Sample for analysis | |
| subject | 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 | |
| Documentation for this format | ||||
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| Specimen | 0..* | Specimen | Sample for analysis | |
| id | Σ | 0..1 | string | 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) Max Binding: AllLanguages: A human language. | |
| 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): Codes providing the status/availability of a specimen. |
| type | Σ | 0..1 | CodeableConcept | Kind of material that forms the specimen Binding: hl7VS-specimenType (example): The type of the specimen. |
| subject | Σ | 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 | 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 | 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 Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure. | |
| bodySite | 0..1 | CodeableConcept | Anatomical collection site Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. | |
| fastingStatus[x] | Σ | 0..1 | Whether or how long patient abstained from food and/or drink Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient. | |
| fastingStatusCodeableConcept | CodeableConcept | |||
| fastingStatusDuration | Duration | |||
| processing | 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): Type indicating the technique 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 | |||
| container | 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): Type of specimen container. | |
| 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 Binding: hl7VS-additivePreservative (example): Substance added to specimen container. | ||
| additiveCodeableConcept | CodeableConcept | |||
| additiveReference | Reference(Substance) | |||
| condition | Σ | 0..* | CodeableConcept | State of the specimen Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen. |
| note | 0..* | Annotation | Comments | |
| Documentation for this format | ||||
Other representations of profile: Schematron
| Path | Conformance | ValueSet |
| Specimen.language | preferred | CommonLanguages Max Binding: AllLanguages |
| 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 | SpecimenContainerType |
| Specimen.container.additive[x] | example | Hl7VSAdditivePreservative |
| Specimen.condition | extensible | Hl7VSSpecimenCondition |
| 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-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-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-5 | Specimen | If a resource is contained in another resource, it SHALL NOT have a security label : contained.meta.security.empty() | |
| dom-6 | Specimen | A resource should have narrative for robust management : text.`div`.exists() | |
| ele-1 | Specimen.meta | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.implicitRules | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.language | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.text | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.extension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | Specimen.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | Specimen.modifierExtension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | Specimen.modifierExtension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | Specimen.identifier | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.accessionIdentifier | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.status | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.type | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.subject | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.receivedTime | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.parent | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.request | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.collection | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.collection.extension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | Specimen.collection.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | Specimen.collection.modifierExtension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | Specimen.collection.modifierExtension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | Specimen.collection.collector | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.collection.collected[x] | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.collection.duration | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.collection.quantity | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.collection.method | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.collection.bodySite | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.collection.fastingStatus[x] | 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.processing.extension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | Specimen.processing.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | Specimen.processing.modifierExtension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | Specimen.processing.modifierExtension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | Specimen.processing.description | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.processing.procedure | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.processing.additive | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.processing.time[x] | 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()) | |
| ele-1 | Specimen.container.extension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | Specimen.container.extension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | Specimen.container.modifierExtension | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ext-1 | Specimen.container.modifierExtension | Must have either extensions or value[x], not both : extension.exists() != value.exists() | |
| ele-1 | Specimen.container.identifier | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.container.description | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.container.type | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.container.capacity | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.container.specimenQuantity | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.container.additive[x] | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.condition | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) | |
| ele-1 | Specimen.note | All FHIR elements must have a @value or children : hasValue() or (children().count() > id.count()) |
IG © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
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