FHIR Osiris Implementation Guide
1.1.0 - trial-implementation
FHIR Osiris Implementation Guide
1.1.0 - trial-implementation
This page is part of the OSIRIS FHIR Implementation Guide (v1.1.0: Release) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version. For a full list of available versions, see the Directory of published versions
| Official URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-biological-sample | Version: 1.1.0 | |||
| Draft as of 2025-04-03 | Computable Name: BiologicalSample | |||
Description of a biological sample coming from an oncology Patient, with its storage condition.
Usage:
Description of Profiles, Differentials, Snapshots and how the different presentations work.
| Nom | Drapeaux | Card. | Type | Description et contraintes |
|---|---|---|---|---|
  Specimen |
0..* | Specimen | Sample for analysis dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources dom-3: 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 dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated dom-5: If a resource is contained in another resource, it SHALL NOT have a security label dom-6: A resource should have narrative for robust management | |
  implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created ele-1: All FHIR elements must have a @value or children |
  Slices pour extension |
1..* | Extension | Extension Slice: Unordered, Open by value:url ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both | |
   extension:BiologicalSampleOrigin |
S | 1..1 | (Complex) | The origin of the sample URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BiologicalSampleOrigin ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
  extension |
0..0 | |||
| url |
1..1 | uri | "https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BiologicalSampleOrigin" | |
  Slices pour value[x] |
1..1 | CodeableConcept | Value of extension Slice: Unordered, Closed by type:$this ele-1: All FHIR elements must have a @value or children | |
  value[x]:valueCodeableConcept |
S | 1..1 | CodeableConcept | The origin of the sample Binding: Biological Sample Origin Value Set (extensible) ele-1: All FHIR elements must have a @value or children |
 text |
Σ | 0..1 | string | Plain text representation of the concept ele-1: All FHIR elements must have a @value or children Required Pattern: Origin of the sample |
| extension:BasedOnCondition |
S | 0..1 | (Complex) | Tumur Pathology Event concerned by the sample URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BasedOnCondition ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
| extension |
0..0 | |||
| url |
1..1 | uri | "https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BasedOnCondition" | |
| Slices pour value[x] |
0..1 | Reference() | Value of extension Slice: Unordered, Closed by type:$this ele-1: All FHIR elements must have a @value or children | |
 value[x]:valueReference |
S | 0..1 | Reference(Tumor Pathology Event) | Value of extension ele-1: All FHIR elements must have a @value or children |
 modifierExtension |
?! | 0..* | Extension | Extensions that cannot be ignored ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
 identifier |
SΣ | 1..1 | Identifier | Identifier of the biological sample ele-1: All FHIR elements must have a @value or children |
| status |
?!Σ | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen. ele-1: All FHIR elements must have a @value or children |
| type |
SΣ | 1..1 | CodeableConcept | The nature of the sample Binding: Biological Sample Nature Value Set (preferred) ele-1: All FHIR elements must have a @value or children |
 subject |
SΣ | 0..1 | Reference(Oncology Patient) | 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 ele-1: All FHIR elements must have a @value or children |
| parent |
S | 0..1 | Reference(Biological Sample) | Identifier of the parent biological sample ele-1: All FHIR elements must have a @value or children |
| collection |
0..1 | BackboneElement | Collection details ele-1: All FHIR elements must have a @value or children | |
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
| Slices pour collected[x] |
Σ | 1..1 | dateTime | Collection time Slice: Unordered, Closed by type:$this ele-1: All FHIR elements must have a @value or children |
| collected[x]:collectedDateTime |
SΣ | 1..1 | dateTime | Collection date ele-1: All FHIR elements must have a @value or children |
| quantity |
S | 0..1 | SimpleQuantity | Percentage of tumor cells ele-1: All FHIR elements must have a @value or children |
| value |
Σ | 0..1 | decimal | Numerical value (with implicit precision) ele-1: All FHIR elements must have a @value or children |
| unit |
Σ | 0..1 | string | Unit representation ele-1: All FHIR elements must have a @value or children Required Pattern: % |
 code |
Σ | 0..1 | code | Coded form of the unit ele-1: All FHIR elements must have a @value or children Required Pattern: C4055283 |
| bodySite |
S | 1..1 | CodeableConcept | Topography of the tumor sample Binding: Topography Value Set (preferred) ele-1: All FHIR elements must have a @value or children |
 condition |
SΣ | 0..1 | CodeableConcept | Storage method Binding: Storage temperature Value Set (extensible) ele-1: All FHIR elements must have a @value or children |
| text |
Σ | 0..1 | string | Plain text representation of the concept ele-1: All FHIR elements must have a @value or children Required Pattern: Storage temperature of the sample. |
| Documentation for this format | ||||
| Path | Conformité | ValueSet | URI |
| Specimen.extension:BiologicalSampleOrigin.value[x]:valueCodeableConcept | extensible | BiologicalSampleOriginhttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleOriginfrom this IG | |
| Specimen.status | required | SpecimenStatushttp://hl7.org/fhir/ValueSet/specimen-status|4.0.1from the FHIR Standard | |
| Specimen.type | preferred | BiologicalSampleNaturehttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleNaturefrom this IG | |
| Specimen.collection.bodySite | preferred | Topographyhttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/Topographyfrom this IG | |
| Specimen.condition | extensible | StorageTemperaturehttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/StorageTemperaturefrom this IG |
This structure is derived from Specimen
| Nom | Drapeaux | Card. | Type | Description et contraintes |
|---|---|---|---|---|
| Specimen |
0..* | Specimen | Sample for analysis | |
| Slices pour extension |
1..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:BiologicalSampleOrigin |
S | 1..1 | (Complex) | The origin of the sample URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BiologicalSampleOrigin |
| Slices pour value[x] |
Content/Rules for all slices | |||
| value[x]:valueCodeableConcept |
1..1 | CodeableConcept | The origin of the sample | |
| extension:BasedOnCondition |
S | 0..1 | (Complex) | Tumur Pathology Event concerned by the sample URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BasedOnCondition |
| Slices pour value[x] |
Content/Rules for all slices | |||
| value[x]:valueReference |
0..1 | Reference(Tumor Pathology Event) | Value of extension | |
 identifier |
S | 1..1 | Identifier | Identifier of the biological sample |
| type |
S | 1..1 | CodeableConcept | The nature of the sample Binding: Biological Sample Nature Value Set (preferred) |
| subject |
S | 0..1 | Reference(Oncology Patient) | 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 |
| parent |
S | 0..1 | Reference(Biological Sample) | Identifier of the parent biological sample |
| collection |
||||
| Slices pour collected[x] |
1..1 | dateTime | Collection time Slice: Unordered, Open by type:$this | |
| collected[x]:collectedDateTime |
S | 1..1 | dateTime | Collection date |
| quantity |
S | 0..1 | SimpleQuantity | Percentage of tumor cells |
| value |
0..1 | decimal | Numerical value (with implicit precision) | |
| unit |
0..1 | string | Unit representation Required Pattern: % | |
| code |
0..1 | code | Coded form of the unit Required Pattern: C4055283 | |
| bodySite |
S | 1..1 | CodeableConcept | Topography of the tumor sample Binding: Topography Value Set (preferred) |
| condition |
S | 0..1 | CodeableConcept | Storage method Binding: Storage temperature Value Set (extensible) |
| text |
0..1 | string | Plain text representation of the concept Required Pattern: Storage temperature of the sample. | |
| Documentation for this format | ||||
| Path | Conformité | ValueSet | URI |
| Specimen.type | preferred | BiologicalSampleNaturehttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleNaturefrom this IG | |
| Specimen.collection.bodySite | preferred | Topographyhttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/Topographyfrom this IG | |
| Specimen.condition | extensible | StorageTemperaturehttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/StorageTemperaturefrom this IG |
| Nom | Drapeaux | Card. | Type | Description et contraintes | ||||
|---|---|---|---|---|---|---|---|---|
| Specimen |
0..* | Specimen | Sample for analysis | |||||
| 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): A human language.
| |||||
| text |
0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained |
0..* | Resource | Contained, inline Resources | |||||
| Slices pour extension |
1..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| extension:BiologicalSampleOrigin |
S | 1..1 | (Complex) | The origin of the sample URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BiologicalSampleOrigin | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..0 | |||||||
| url |
1..1 | uri | "https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BiologicalSampleOrigin" | |||||
| Slices pour value[x] |
1..1 | CodeableConcept | Value of extension Slice: Unordered, Closed by type:$this | |||||
| value[x]:valueCodeableConcept |
S | 1..1 | CodeableConcept | The origin of the sample Binding: Biological Sample Origin Value Set (extensible) | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
Σ | 0..* | Coding | Code defined by a terminology system | ||||
| text |
Σ | 0..1 | string | Plain text representation of the concept Required Pattern: Origin of the sample | ||||
| extension:BasedOnCondition |
S | 0..1 | (Complex) | Tumur Pathology Event concerned by the sample URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BasedOnCondition | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..0 | |||||||
| url |
1..1 | uri | "https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BasedOnCondition" | |||||
| Slices pour value[x] |
0..1 | Reference() | Value of extension Slice: Unordered, Closed by type:$this | |||||
| value[x]:valueReference |
S | 0..1 | Reference(Tumor Pathology Event) | Value of extension | ||||
| modifierExtension |
?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
SΣ | 1..1 | Identifier | Identifier of the biological sample | ||||
| 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 |
SΣ | 1..1 | CodeableConcept | The nature of the sample Binding: Biological Sample Nature Value Set (preferred) | ||||
| subject |
SΣ | 0..1 | Reference(Oncology Patient) | 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 |
S | 0..1 | Reference(Biological Sample) | Identifier of the parent biological sample | ||||
| 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 | ||||
| Slices pour collected[x] |
Σ | 1..1 | dateTime | Collection time Slice: Unordered, Closed by type:$this | ||||
| collected[x]:collectedDateTime |
SΣ | 1..1 | dateTime | Collection date | ||||
| duration |
Σ | 0..1 | Duration | How long it took to collect specimen | ||||
| quantity |
S | 0..1 | SimpleQuantity | Percentage of tumor cells | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| value |
Σ | 0..1 | decimal | Numerical value (with implicit precision) | ||||
| unit |
Σ | 0..1 | string | Unit representation Required Pattern: % | ||||
| system |
ΣC | 0..1 | uri | System that defines coded unit form | ||||
| code |
Σ | 0..1 | code | Coded form of the unit Required Pattern: C4055283 | ||||
| method |
0..1 | CodeableConcept | Technique used to perform collection Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure. | |||||
| bodySite |
S | 1..1 | CodeableConcept | Topography of the tumor sample Binding: Topography Value Set (preferred) | ||||
 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 |
SΣ | 0..1 | CodeableConcept | Storage method Binding: Storage temperature Value Set (extensible) | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
Σ | 0..* | Coding | Code defined by a terminology system | ||||
| text |
Σ | 0..1 | string | Plain text representation of the concept Required Pattern: Storage temperature of the sample. | ||||
| note |
0..* | Annotation | Comments | |||||
| Documentation for this format | ||||||||
| Path | Conformité | ValueSet | URI | |||
| Specimen.language | preferred | CommonLanguageshttp://hl7.org/fhir/ValueSet/languagesfrom the FHIR Standard
| ||||
| Specimen.extension:BiologicalSampleOrigin.value[x]:valueCodeableConcept | extensible | BiologicalSampleOriginhttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleOriginfrom this IG | ||||
| Specimen.status | required | SpecimenStatushttp://hl7.org/fhir/ValueSet/specimen-status|4.0.1from the FHIR Standard | ||||
| Specimen.type | preferred | BiologicalSampleNaturehttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleNaturefrom this IG | ||||
| Specimen.collection.method | example | FHIRSpecimenCollectionMethodhttp://hl7.org/fhir/ValueSet/specimen-collection-methodfrom the FHIR Standard | ||||
| Specimen.collection.bodySite | preferred | Topographyhttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/Topographyfrom this IG | ||||
| Specimen.collection.fastingStatus[x] | extensible | Hl7VSRelevantClincialInformationhttp://terminology.hl7.org/ValueSet/v2-0916 | ||||
| Specimen.processing.procedure | example | SpecimenProcessingProcedurehttp://hl7.org/fhir/ValueSet/specimen-processing-procedurefrom the FHIR Standard | ||||
| Specimen.container.type | example | SpecimenContainerTypehttp://hl7.org/fhir/ValueSet/specimen-container-typefrom the FHIR Standard | ||||
| Specimen.container.additive[x] | example | Hl7VSAdditivePreservativehttp://terminology.hl7.org/ValueSet/v2-0371 | ||||
| Specimen.condition | extensible | StorageTemperaturehttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/StorageTemperaturefrom this IG |
This structure is derived from Specimen
Résumé
Mandatory: 4 elements(3 nested mandatory elements)
Must-Support: 10 elements
Structures
This structure refers to these other structures:
Extensions
This structure refers to these extensions:
Slices
This structure defines the following Slices:
Key Elements View
| Nom | Drapeaux | Card. | Type | Description et contraintes |
|---|---|---|---|---|
| Specimen |
0..* | Specimen | Sample for analysis dom-2: If the resource is contained in another resource, it SHALL NOT contain nested Resources dom-3: 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 dom-4: If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated dom-5: If a resource is contained in another resource, it SHALL NOT have a security label dom-6: A resource should have narrative for robust management | |
| implicitRules |
?!Σ | 0..1 | uri | A set of rules under which this content was created ele-1: All FHIR elements must have a @value or children |
| Slices pour extension |
1..* | Extension | Extension Slice: Unordered, Open by value:url ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both | |
| extension:BiologicalSampleOrigin |
S | 1..1 | (Complex) | The origin of the sample URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BiologicalSampleOrigin ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
| extension |
0..0 | |||
| url |
1..1 | uri | "https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BiologicalSampleOrigin" | |
| Slices pour value[x] |
1..1 | CodeableConcept | Value of extension Slice: Unordered, Closed by type:$this ele-1: All FHIR elements must have a @value or children | |
| value[x]:valueCodeableConcept |
S | 1..1 | CodeableConcept | The origin of the sample Binding: Biological Sample Origin Value Set (extensible) ele-1: All FHIR elements must have a @value or children |
| text |
Σ | 0..1 | string | Plain text representation of the concept ele-1: All FHIR elements must have a @value or children Required Pattern: Origin of the sample |
| extension:BasedOnCondition |
S | 0..1 | (Complex) | Tumur Pathology Event concerned by the sample URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BasedOnCondition ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
| extension |
0..0 | |||
| url |
1..1 | uri | "https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BasedOnCondition" | |
| Slices pour value[x] |
0..1 | Reference() | Value of extension Slice: Unordered, Closed by type:$this ele-1: All FHIR elements must have a @value or children | |
| value[x]:valueReference |
S | 0..1 | Reference(Tumor Pathology Event) | Value of extension ele-1: All FHIR elements must have a @value or children |
| modifierExtension |
?! | 0..* | Extension | Extensions that cannot be ignored ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
| identifier |
SΣ | 1..1 | Identifier | Identifier of the biological sample ele-1: All FHIR elements must have a @value or children |
| status |
?!Σ | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen. ele-1: All FHIR elements must have a @value or children |
| type |
SΣ | 1..1 | CodeableConcept | The nature of the sample Binding: Biological Sample Nature Value Set (preferred) ele-1: All FHIR elements must have a @value or children |
| subject |
SΣ | 0..1 | Reference(Oncology Patient) | Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device ele-1: All FHIR elements must have a @value or children |
| parent |
S | 0..1 | Reference(Biological Sample) | Identifier of the parent biological sample ele-1: All FHIR elements must have a @value or children |
| collection |
0..1 | BackboneElement | Collection details ele-1: All FHIR elements must have a @value or children | |
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both |
| Slices pour collected[x] |
Σ | 1..1 | dateTime | Collection time Slice: Unordered, Closed by type:$this ele-1: All FHIR elements must have a @value or children |
| collected[x]:collectedDateTime |
SΣ | 1..1 | dateTime | Collection date ele-1: All FHIR elements must have a @value or children |
| quantity |
S | 0..1 | SimpleQuantity | Percentage of tumor cells ele-1: All FHIR elements must have a @value or children |
| value |
Σ | 0..1 | decimal | Numerical value (with implicit precision) ele-1: All FHIR elements must have a @value or children |
| unit |
Σ | 0..1 | string | Unit representation ele-1: All FHIR elements must have a @value or children Required Pattern: % |
| code |
Σ | 0..1 | code | Coded form of the unit ele-1: All FHIR elements must have a @value or children Required Pattern: C4055283 |
| bodySite |
S | 1..1 | CodeableConcept | Topography of the tumor sample Binding: Topography Value Set (preferred) ele-1: All FHIR elements must have a @value or children |
| condition |
SΣ | 0..1 | CodeableConcept | Storage method Binding: Storage temperature Value Set (extensible) ele-1: All FHIR elements must have a @value or children |
| text |
Σ | 0..1 | string | Plain text representation of the concept ele-1: All FHIR elements must have a @value or children Required Pattern: Storage temperature of the sample. |
| Documentation for this format | ||||
| Path | Conformité | ValueSet | URI |
| Specimen.extension:BiologicalSampleOrigin.value[x]:valueCodeableConcept | extensible | BiologicalSampleOriginhttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleOriginfrom this IG | |
| Specimen.status | required | SpecimenStatushttp://hl7.org/fhir/ValueSet/specimen-status|4.0.1from the FHIR Standard | |
| Specimen.type | preferred | BiologicalSampleNaturehttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleNaturefrom this IG | |
| Specimen.collection.bodySite | preferred | Topographyhttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/Topographyfrom this IG | |
| Specimen.condition | extensible | StorageTemperaturehttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/StorageTemperaturefrom this IG |
Differential View
This structure is derived from Specimen
| Nom | Drapeaux | Card. | Type | Description et contraintes |
|---|---|---|---|---|
| Specimen |
0..* | Specimen | Sample for analysis | |
| Slices pour extension |
1..* | Extension | Extension Slice: Unordered, Open by value:url | |
| extension:BiologicalSampleOrigin |
S | 1..1 | (Complex) | The origin of the sample URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BiologicalSampleOrigin |
| Slices pour value[x] |
Content/Rules for all slices | |||
| value[x]:valueCodeableConcept |
1..1 | CodeableConcept | The origin of the sample | |
| extension:BasedOnCondition |
S | 0..1 | (Complex) | Tumur Pathology Event concerned by the sample URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BasedOnCondition |
| Slices pour value[x] |
Content/Rules for all slices | |||
| value[x]:valueReference |
0..1 | Reference(Tumor Pathology Event) | Value of extension | |
| identifier |
S | 1..1 | Identifier | Identifier of the biological sample |
| type |
S | 1..1 | CodeableConcept | The nature of the sample Binding: Biological Sample Nature Value Set (preferred) |
| subject |
S | 0..1 | Reference(Oncology Patient) | 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 |
| parent |
S | 0..1 | Reference(Biological Sample) | Identifier of the parent biological sample |
| collection |
||||
| Slices pour collected[x] |
1..1 | dateTime | Collection time Slice: Unordered, Open by type:$this | |
| collected[x]:collectedDateTime |
S | 1..1 | dateTime | Collection date |
| quantity |
S | 0..1 | SimpleQuantity | Percentage of tumor cells |
| value |
0..1 | decimal | Numerical value (with implicit precision) | |
| unit |
0..1 | string | Unit representation Required Pattern: % | |
| code |
0..1 | code | Coded form of the unit Required Pattern: C4055283 | |
| bodySite |
S | 1..1 | CodeableConcept | Topography of the tumor sample Binding: Topography Value Set (preferred) |
| condition |
S | 0..1 | CodeableConcept | Storage method Binding: Storage temperature Value Set (extensible) |
| text |
0..1 | string | Plain text representation of the concept Required Pattern: Storage temperature of the sample. | |
| Documentation for this format | ||||
| Path | Conformité | ValueSet | URI |
| Specimen.type | preferred | BiologicalSampleNaturehttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleNaturefrom this IG | |
| Specimen.collection.bodySite | preferred | Topographyhttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/Topographyfrom this IG | |
| Specimen.condition | extensible | StorageTemperaturehttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/StorageTemperaturefrom this IG |
Snapshot View
| Nom | Drapeaux | Card. | Type | Description et contraintes | ||||
|---|---|---|---|---|---|---|---|---|
| Specimen |
0..* | Specimen | Sample for analysis | |||||
| 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): A human language.
| |||||
| text |
0..1 | Narrative | Text summary of the resource, for human interpretation | |||||
| contained |
0..* | Resource | Contained, inline Resources | |||||
| Slices pour extension |
1..* | Extension | Extension Slice: Unordered, Open by value:url | |||||
| extension:BiologicalSampleOrigin |
S | 1..1 | (Complex) | The origin of the sample URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BiologicalSampleOrigin | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..0 | |||||||
| url |
1..1 | uri | "https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BiologicalSampleOrigin" | |||||
| Slices pour value[x] |
1..1 | CodeableConcept | Value of extension Slice: Unordered, Closed by type:$this | |||||
| value[x]:valueCodeableConcept |
S | 1..1 | CodeableConcept | The origin of the sample Binding: Biological Sample Origin Value Set (extensible) | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
Σ | 0..* | Coding | Code defined by a terminology system | ||||
| text |
Σ | 0..1 | string | Plain text representation of the concept Required Pattern: Origin of the sample | ||||
| extension:BasedOnCondition |
S | 0..1 | (Complex) | Tumur Pathology Event concerned by the sample URL: https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BasedOnCondition | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..0 | |||||||
| url |
1..1 | uri | "https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BasedOnCondition" | |||||
| Slices pour value[x] |
0..1 | Reference() | Value of extension Slice: Unordered, Closed by type:$this | |||||
| value[x]:valueReference |
S | 0..1 | Reference(Tumor Pathology Event) | Value of extension | ||||
| modifierExtension |
?! | 0..* | Extension | Extensions that cannot be ignored | ||||
| identifier |
SΣ | 1..1 | Identifier | Identifier of the biological sample | ||||
| accessionIdentifier |
Σ | 0..1 | Identifier | Identifier assigned by the lab | ||||
| status |
?!Σ | 0..1 | code | available | unavailable | unsatisfactory | entered-in-error Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen. | ||||
| type |
SΣ | 1..1 | CodeableConcept | The nature of the sample Binding: Biological Sample Nature Value Set (preferred) | ||||
| subject |
SΣ | 0..1 | Reference(Oncology Patient) | Where the specimen came from. This may be from patient(s), from a location (e.g., the source of an environmental sample), or a sampling of a substance or a device | ||||
| receivedTime |
Σ | 0..1 | dateTime | The time when specimen was received for processing | ||||
| parent |
S | 0..1 | Reference(Biological Sample) | Identifier of the parent biological sample | ||||
| request |
0..* | Reference(ServiceRequest) | Why the specimen was collected | |||||
| collection |
0..1 | BackboneElement | Collection details | |||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations | |||||
| modifierExtension |
?!Σ | 0..* | Extension | Extensions that cannot be ignored even if unrecognized | ||||
| collector |
Σ | 0..1 | Reference(Practitioner | PractitionerRole) | Who collected the specimen | ||||
| Slices pour collected[x] |
Σ | 1..1 | dateTime | Collection time Slice: Unordered, Closed by type:$this | ||||
| collected[x]:collectedDateTime |
SΣ | 1..1 | dateTime | Collection date | ||||
| duration |
Σ | 0..1 | Duration | How long it took to collect specimen | ||||
| quantity |
S | 0..1 | SimpleQuantity | Percentage of tumor cells | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| value |
Σ | 0..1 | decimal | Numerical value (with implicit precision) | ||||
| unit |
Σ | 0..1 | string | Unit representation Required Pattern: % | ||||
| system |
ΣC | 0..1 | uri | System that defines coded unit form | ||||
| code |
Σ | 0..1 | code | Coded form of the unit Required Pattern: C4055283 | ||||
| method |
0..1 | CodeableConcept | Technique used to perform collection Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure. | |||||
| bodySite |
S | 1..1 | CodeableConcept | Topography of the tumor sample Binding: Topography Value Set (preferred) | ||||
| 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 |
SΣ | 0..1 | CodeableConcept | Storage method Binding: Storage temperature Value Set (extensible) | ||||
| id |
0..1 | string | Unique id for inter-element referencing | |||||
| extension |
0..* | Extension | Additional content defined by implementations Slice: Unordered, Open by value:url | |||||
| coding |
Σ | 0..* | Coding | Code defined by a terminology system | ||||
| text |
Σ | 0..1 | string | Plain text representation of the concept Required Pattern: Storage temperature of the sample. | ||||
| note |
0..* | Annotation | Comments | |||||
| Documentation for this format | ||||||||
| Path | Conformité | ValueSet | URI | |||
| Specimen.language | preferred | CommonLanguageshttp://hl7.org/fhir/ValueSet/languagesfrom the FHIR Standard
| ||||
| Specimen.extension:BiologicalSampleOrigin.value[x]:valueCodeableConcept | extensible | BiologicalSampleOriginhttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleOriginfrom this IG | ||||
| Specimen.status | required | SpecimenStatushttp://hl7.org/fhir/ValueSet/specimen-status|4.0.1from the FHIR Standard | ||||
| Specimen.type | preferred | BiologicalSampleNaturehttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleNaturefrom this IG | ||||
| Specimen.collection.method | example | FHIRSpecimenCollectionMethodhttp://hl7.org/fhir/ValueSet/specimen-collection-methodfrom the FHIR Standard | ||||
| Specimen.collection.bodySite | preferred | Topographyhttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/Topographyfrom this IG | ||||
| Specimen.collection.fastingStatus[x] | extensible | Hl7VSRelevantClincialInformationhttp://terminology.hl7.org/ValueSet/v2-0916 | ||||
| Specimen.processing.procedure | example | SpecimenProcessingProcedurehttp://hl7.org/fhir/ValueSet/specimen-processing-procedurefrom the FHIR Standard | ||||
| Specimen.container.type | example | SpecimenContainerTypehttp://hl7.org/fhir/ValueSet/specimen-container-typefrom the FHIR Standard | ||||
| Specimen.container.additive[x] | example | Hl7VSAdditivePreservativehttp://terminology.hl7.org/ValueSet/v2-0371 | ||||
| Specimen.condition | extensible | StorageTemperaturehttps://ig-osiris.cancer.fr/ig/osiris/ValueSet/StorageTemperaturefrom this IG |
This structure is derived from Specimen
Résumé
Mandatory: 4 elements(3 nested mandatory elements)
Must-Support: 10 elements
Structures
This structure refers to these other structures:
Extensions
This structure refers to these extensions:
Slices
This structure defines the following Slices:
Other representations of profile: CSV, Excel, Schematron