FHIR Osiris Implementation Guide
1.1.0 - trial-implementation

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## Resource Profile: Biological Sample

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:

- Refer to this Resource Profile: Biological Sample and Sequencing Analysis
- Examples for this Resource Profile: Specimen/fhir-osiris-example-biologicalsample-1 and Specimen/fhir-osiris-example-biologicalsample-2

### Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

- Key Elements Table
- Differential Table
- Snapshot Table
- Statistics/References
- All

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 | S Σ | 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 | S Σ | 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 | S Σ | 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 | S Σ | 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 | S Σ | 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

#### Terminology Bindings

Path | Conformité | ValueSet | URI
Specimen.extension:BiologicalSampleOrigin.value[x]:valueCodeableConcept | extensible | BiologicalSampleOrigin `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleOrigin` from this IG
Specimen.status | required | SpecimenStatus `http://hl7.org/fhir/ValueSet/specimen-status|4.0.1` from the FHIR Standard
Specimen.type | preferred | BiologicalSampleNature `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleNature` from this IG
Specimen.collection.bodySite | preferred | Topography `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/Topography` from this IG
Specimen.condition | extensible | StorageTemperature `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/StorageTemperature` from 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

#### Terminology Bindings (Differential)

Path | Conformité | ValueSet | URI
Specimen.type | preferred | BiologicalSampleNature `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleNature` from this IG
Specimen.collection.bodySite | preferred | Topography `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/Topography` from this IG
Specimen.condition | extensible | StorageTemperature `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/StorageTemperature` from 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.
Bindings Additionnels | But
AllLanguages | Binding Max
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 | S Σ | 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 | S Σ | 1..1 | CodeableConcept | The nature of the sample Binding: Biological Sample Nature Value Set (preferred)
subject | S Σ | 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 | S Σ | 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 | Σ C | 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 | S Σ | 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

#### Terminology Bindings

Path | Conformité | ValueSet | URI
Specimen.language | preferred | CommonLanguages `http://hl7.org/fhir/ValueSet/languages` from the FHIR Standard
Bindings Additionnels | But
AllLanguages | Binding Max
Specimen.extension:BiologicalSampleOrigin.value[x]:valueCodeableConcept | extensible | BiologicalSampleOrigin `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleOrigin` from this IG
Specimen.status | required | SpecimenStatus `http://hl7.org/fhir/ValueSet/specimen-status|4.0.1` from the FHIR Standard
Specimen.type | preferred | BiologicalSampleNature `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleNature` from this IG
Specimen.collection.method | example | FHIRSpecimenCollectionMethod `http://hl7.org/fhir/ValueSet/specimen-collection-method` from the FHIR Standard
Specimen.collection.bodySite | preferred | Topography `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/Topography` from this IG
Specimen.collection.fastingStatus[x] | extensible | Hl7VSRelevantClincialInformation `http://terminology.hl7.org/ValueSet/v2-0916`
Specimen.processing.procedure | example | SpecimenProcessingProcedure `http://hl7.org/fhir/ValueSet/specimen-processing-procedure` from the FHIR Standard
Specimen.container.type | example | SpecimenContainerType `http://hl7.org/fhir/ValueSet/specimen-container-type` from the FHIR Standard
Specimen.container.additive[x] | example | Hl7VSAdditivePreservative `http://terminology.hl7.org/ValueSet/v2-0371`
Specimen.condition | extensible | StorageTemperature `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/StorageTemperature` from 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:

- Tumor Pathology Event (https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/tumor-pathology-event)
- Oncology Patient (https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-patient)
- Biological Sample (https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-biological-sample)

Extensions

This structure refers to these extensions:

- https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BiologicalSampleOrigin
- https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BasedOnCondition

Slices

This structure defines the following Slices:

- The element 1 is sliced based on the value of Specimen.collection.collected[x]

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 | S Σ | 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 | S Σ | 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 | S Σ | 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 | S Σ | 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 | S Σ | 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

#### Terminology Bindings

Path | Conformité | ValueSet | URI
Specimen.extension:BiologicalSampleOrigin.value[x]:valueCodeableConcept | extensible | BiologicalSampleOrigin `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleOrigin` from this IG
Specimen.status | required | SpecimenStatus `http://hl7.org/fhir/ValueSet/specimen-status|4.0.1` from the FHIR Standard
Specimen.type | preferred | BiologicalSampleNature `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleNature` from this IG
Specimen.collection.bodySite | preferred | Topography `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/Topography` from this IG
Specimen.condition | extensible | StorageTemperature `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/StorageTemperature` from 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

#### Terminology Bindings (Differential)

Path | Conformité | ValueSet | URI
Specimen.type | preferred | BiologicalSampleNature `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleNature` from this IG
Specimen.collection.bodySite | preferred | Topography `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/Topography` from this IG
Specimen.condition | extensible | StorageTemperature `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/StorageTemperature` from 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.
Bindings Additionnels | But
AllLanguages | Binding Max
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 | S Σ | 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 | S Σ | 1..1 | CodeableConcept | The nature of the sample Binding: Biological Sample Nature Value Set (preferred)
subject | S Σ | 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 | S Σ | 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 | Σ C | 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 | S Σ | 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

#### Terminology Bindings

Path | Conformité | ValueSet | URI
Specimen.language | preferred | CommonLanguages `http://hl7.org/fhir/ValueSet/languages` from the FHIR Standard
Bindings Additionnels | But
AllLanguages | Binding Max
Specimen.extension:BiologicalSampleOrigin.value[x]:valueCodeableConcept | extensible | BiologicalSampleOrigin `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleOrigin` from this IG
Specimen.status | required | SpecimenStatus `http://hl7.org/fhir/ValueSet/specimen-status|4.0.1` from the FHIR Standard
Specimen.type | preferred | BiologicalSampleNature `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/BiologicalSampleNature` from this IG
Specimen.collection.method | example | FHIRSpecimenCollectionMethod `http://hl7.org/fhir/ValueSet/specimen-collection-method` from the FHIR Standard
Specimen.collection.bodySite | preferred | Topography `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/Topography` from this IG
Specimen.collection.fastingStatus[x] | extensible | Hl7VSRelevantClincialInformation `http://terminology.hl7.org/ValueSet/v2-0916`
Specimen.processing.procedure | example | SpecimenProcessingProcedure `http://hl7.org/fhir/ValueSet/specimen-processing-procedure` from the FHIR Standard
Specimen.container.type | example | SpecimenContainerType `http://hl7.org/fhir/ValueSet/specimen-container-type` from the FHIR Standard
Specimen.container.additive[x] | example | Hl7VSAdditivePreservative `http://terminology.hl7.org/ValueSet/v2-0371`
Specimen.condition | extensible | StorageTemperature `https://ig-osiris.cancer.fr/ig/osiris/ValueSet/StorageTemperature` from 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:

- Tumor Pathology Event (https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/tumor-pathology-event)
- Oncology Patient (https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-patient)
- Biological Sample (https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/onco-biological-sample)

Extensions

This structure refers to these extensions:

- https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BiologicalSampleOrigin
- https://ig-osiris.cancer.fr/ig/osiris/StructureDefinition/BasedOnCondition

Slices

This structure defines the following Slices:

- The element 1 is sliced based on the value of Specimen.collection.collected[x]

Other representations of profile: CSV, Excel, Schematron