Genomics Reporting Implementation Guide (STU1)
This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 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 
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 | string | Logical id of this artifact |
 meta | ΣI | 0..1 | Meta | Metadata about the resource |
| implicitRules | ?!ΣI | 0..1 | uri | A set of rules under which this content was created |
| language | I | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred) Max Binding: AllLanguages |
| text | I | 0..1 | Narrative | Text summary of the resource, for human interpretation |
 contained | 0..* | Resource | Contained, inline Resources | |
 extension | I | 0..* | Extension | Additional content defined by implementations |
 modifierExtension | ?!I | 0..* | Extension | Extensions that cannot be ignored |
| identifier | ΣI | 0..* | Identifier | External Identifier |
| accessionIdentifier | ΣI | 0..1 | Identifier | Identifier assigned by the lab |
| status | ?!ΣI | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required) |
| type | ΣI | 0..1 | CodeableConcept | Kind of material that forms the specimen Binding: v2 Specimen Type (example) |
 subject | ΣI | 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 | ΣI | 0..1 | dateTime | The time when specimen was received for processing |
| parent | I | 0..* | Reference(Specimen) | Specimen from which this specimen originated |
| request | I | 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 | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| collector | ΣI | 0..1 | Reference(Practitioner | PractitionerRole) | Who collected the specimen |
 collected[x] | ΣI | 0..1 | Collection time | |
| collectedDateTime | dateTime | |||
 collectedPeriod | Period | |||
| duration | ΣI | 0..1 | Duration | How long it took to collect specimen |
| quantity | I | 0..1 | SimpleQuantity | The quantity of specimen collected |
| method | I | 0..1 | CodeableConcept | Technique used to perform collection Binding: FHIRSpecimenCollectionMethod (example) |
| bodySite | I | 0..1 | CodeableConcept | Anatomical collection site Binding: SNOMEDCTBodyStructures (example) |
| fastingStatus[x] | ΣI | 0..1 | Whether or how long patient abstained from food and/or drink Binding: v2 Relevant Clincial Information (extensible) | |
 fastingStatusCodeableConcept | CodeableConcept | |||
| fastingStatusDuration | Duration | |||
| processing | I | 0..* | BackboneElement | Processing and processing step details |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| description | I | 0..1 | string | Textual description of procedure |
| procedure | I | 0..1 | CodeableConcept | Indicates the treatment step applied to the specimen Binding: SpecimenProcessingProcedure (example) |
| additive | I | 0..* | Reference(Substance) | Material used in the processing step |
| time[x] | I | 0..1 | Date and time of specimen processing | |
| timeDateTime | dateTime | |||
| timePeriod | Period | |||
| container | I | 0..* | BackboneElement | Direct container of specimen (tube/slide, etc.) |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| identifier | ΣI | 0..* | Identifier | Id for the container |
| description | I | 0..1 | string | Textual description of the container |
| type | I | 0..1 | CodeableConcept | Kind of container directly associated with specimen Binding: SpecimenContainerType (example) |
| capacity | I | 0..1 | SimpleQuantity | Container volume or size |
| specimenQuantity | I | 0..1 | SimpleQuantity | Quantity of specimen within container |
| additive[x] | I | 0..1 | Additive associated with container Binding: v2 Additive (example) | |
| additiveCodeableConcept | CodeableConcept | |||
| additiveReference | Reference(Substance) | |||
| condition | ΣI | 0..* | CodeableConcept | State of the specimen Binding: v2 Specimen Condition (extensible) |
| note | I | 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 | string | Logical id of this artifact |
| meta | ΣI | 0..1 | Meta | Metadata about the resource |
| implicitRules | ?!ΣI | 0..1 | uri | A set of rules under which this content was created |
| language | I | 0..1 | code | Language of the resource content Binding: CommonLanguages (preferred) Max Binding: AllLanguages |
| text | I | 0..1 | Narrative | Text summary of the resource, for human interpretation |
| contained | 0..* | Resource | Contained, inline Resources | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!I | 0..* | Extension | Extensions that cannot be ignored |
| identifier | ΣI | 0..* | Identifier | External Identifier |
| accessionIdentifier | ΣI | 0..1 | Identifier | Identifier assigned by the lab |
| status | ?!ΣI | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required) |
| type | ΣI | 0..1 | CodeableConcept | Kind of material that forms the specimen Binding: v2 Specimen Type (example) |
| subject | ΣI | 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 | ΣI | 0..1 | dateTime | The time when specimen was received for processing |
| parent | I | 0..* | Reference(Specimen) | Specimen from which this specimen originated |
| request | I | 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 | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| collector | ΣI | 0..1 | Reference(Practitioner | PractitionerRole) | Who collected the specimen |
| collected[x] | ΣI | 0..1 | Collection time | |
| collectedDateTime | dateTime | |||
| collectedPeriod | Period | |||
| duration | ΣI | 0..1 | Duration | How long it took to collect specimen |
| quantity | I | 0..1 | SimpleQuantity | The quantity of specimen collected |
| method | I | 0..1 | CodeableConcept | Technique used to perform collection Binding: FHIRSpecimenCollectionMethod (example) |
| bodySite | I | 0..1 | CodeableConcept | Anatomical collection site Binding: SNOMEDCTBodyStructures (example) |
| fastingStatus[x] | ΣI | 0..1 | Whether or how long patient abstained from food and/or drink Binding: v2 Relevant Clincial Information (extensible) | |
| fastingStatusCodeableConcept | CodeableConcept | |||
| fastingStatusDuration | Duration | |||
| processing | I | 0..* | BackboneElement | Processing and processing step details |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| description | I | 0..1 | string | Textual description of procedure |
| procedure | I | 0..1 | CodeableConcept | Indicates the treatment step applied to the specimen Binding: SpecimenProcessingProcedure (example) |
| additive | I | 0..* | Reference(Substance) | Material used in the processing step |
| time[x] | I | 0..1 | Date and time of specimen processing | |
| timeDateTime | dateTime | |||
| timePeriod | Period | |||
| container | I | 0..* | BackboneElement | Direct container of specimen (tube/slide, etc.) |
| id | 0..1 | string | Unique id for inter-element referencing | |
| extension | I | 0..* | Extension | Additional content defined by implementations |
| modifierExtension | ?!ΣI | 0..* | Extension | Extensions that cannot be ignored even if unrecognized |
| identifier | ΣI | 0..* | Identifier | Id for the container |
| description | I | 0..1 | string | Textual description of the container |
| type | I | 0..1 | CodeableConcept | Kind of container directly associated with specimen Binding: SpecimenContainerType (example) |
| capacity | I | 0..1 | SimpleQuantity | Container volume or size |
| specimenQuantity | I | 0..1 | SimpleQuantity | Quantity of specimen within container |
| additive[x] | I | 0..1 | Additive associated with container Binding: v2 Additive (example) | |
| additiveCodeableConcept | CodeableConcept | |||
| additiveReference | Reference(Substance) | |||
| condition | ΣI | 0..* | CodeableConcept | State of the specimen Binding: v2 Specimen Condition (extensible) |
| note | I | 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 | v2.0487 |
| Specimen.collection.method | example | FHIRSpecimenCollectionMethod |
| Specimen.collection.bodySite | example | SNOMEDCTBodyStructures |
| Specimen.collection.fastingStatus[x] | extensible | v2.0916 |
| Specimen.processing.procedure | example | SpecimenProcessingProcedure |
| Specimen.container.type | example | SpecimenContainerType |
| Specimen.container.additive[x] | example | v2.0371 |
| 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-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 © 2017+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.0.0 based on FHIR 4.0.1. Generated 2019-11-20
Links: Table of Contents |
QA Report | Search |
Version History |
|
Propose a change