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PROTECT-CHILD Pediatric Transplant Data Implementation Guide
0.1.0-ci-build -

PROTECT-CHILD Pediatric Transplant Data Implementation Guide
0.1.0-ci-build - ci-build

PROTECT-CHILD Pediatric Transplant Data Implementation Guide, published by Protect Child. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/hl7-eu/protect-child/ and changes regularly. See the Directory of published versions

Resource Profile: Biological Sample

Official URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample Version: 0.1.0-ci-build
Draft as of 2026-02-09 Computable Name: BioSample

Biological sample linked to transplant patients and omics studies, aligned with the bio_sample table.

Usages:

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

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

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen 0..* Specimen Sample for analysis
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:genomic_test_id S 0..1 Reference(Genomic Test) genomic_test_id – Reference to GenomicTest
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-genomic-test-ref
.... extension:epigenome_study_id S 0..1 Reference(Epigenome Study) epigenome_study_id – Reference to EpigenomeStudy
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-epigenome-study-ref
.... extension:methylomic_study_id S 0..1 Reference(Methylomic Study) methylomic_study_id – Reference to MethylomicStudy
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-methylomic-study-ref
.... extension:send_ingemm_date S 1..1 date send_ingemm_date – date sample sent to INGEMM
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-send-ingemm-date
.... extension:dna_concentration SC 0..1 decimal dna_concentration – DNA concentration (float, ≥ 0)
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-dna-concentration
Constraints: biosample-dna-concentration-nonnegative
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
.... use ?!Σ 0..1 code usual | official | temp | secondary | old (If known)
Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .
.... system Σ 1..1 uri The namespace for the identifier value
Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/biosample-id
.... value Σ 1..1 string The value that is unique
Example General: 123456
... 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 tissue_type – type of tissue sampled
Binding: BioSample Tissue Type ValueSet (required): The type of the specimen.
.... text Σ 1..1 string Plain text representation of the concept
... subject SΣ 1..1 Reference(Transplant Recipient) patient_id – reference to the transplant recipient
... collection S 1..1 BackboneElement Sample collection details
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... collected[x] Σ 1..1 dateTime collection_date – sample collection date

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Specimen.identifier.​use Base required IdentifierUse 📍4.0.1 FHIR Std.
Specimen.status Base required SpecimenStatus 📍4.0.1 FHIR Std.
Specimen.type Base required BioSample Tissue Type ValueSet 📦0.1.0-ci-build This IG

Constraints

Id Grade Path(s) Description Expression
biosample-dna-concentration-nonnegative error Specimen.extension:dna_concentration DNA concentration must be zero or positive. valueDecimal >= 0
dom-2 error Specimen If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error 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 error 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 error Specimen If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Specimen A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

This structure is derived from Specimen

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen 0..* Specimen Sample for analysis
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:genomic_test_id S 0..1 Reference(Genomic Test) genomic_test_id – Reference to GenomicTest
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-genomic-test-ref
.... extension:epigenome_study_id S 0..1 Reference(Epigenome Study) epigenome_study_id – Reference to EpigenomeStudy
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-epigenome-study-ref
.... extension:methylomic_study_id S 0..1 Reference(Methylomic Study) methylomic_study_id – Reference to MethylomicStudy
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-methylomic-study-ref
.... extension:send_ingemm_date S 1..1 date send_ingemm_date – date sample sent to INGEMM
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-send-ingemm-date
.... extension:dna_concentration S 0..1 decimal dna_concentration – DNA concentration (float, ≥ 0)
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-dna-concentration
... identifier S 1..1 Identifier bio_sample_id – primary identifier for the biological sample
.... system 1..1 uri The namespace for the identifier value
Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/biosample-id
.... value 1..1 string The value that is unique
... type S 1..1 CodeableConcept tissue_type – type of tissue sampled
Binding: BioSample Tissue Type ValueSet (required): The type of the specimen.
.... text 1..1 string Plain text representation of the concept
... collection S 1..1 BackboneElement Sample collection details
.... collected[x] 1..1 dateTime collection_date – sample collection date

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Specimen.type Base required BioSample Tissue Type ValueSet 📦0.1.0-ci-build This IG
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:genomic_test_id S 0..1 Reference(Genomic Test) genomic_test_id – Reference to GenomicTest
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-genomic-test-ref
.... extension:epigenome_study_id S 0..1 Reference(Epigenome Study) epigenome_study_id – Reference to EpigenomeStudy
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-epigenome-study-ref
.... extension:methylomic_study_id S 0..1 Reference(Methylomic Study) methylomic_study_id – Reference to MethylomicStudy
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-methylomic-study-ref
.... extension:send_ingemm_date S 1..1 date send_ingemm_date – date sample sent to INGEMM
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-send-ingemm-date
.... extension:dna_concentration SC 0..1 decimal dna_concentration – DNA concentration (float, ≥ 0)
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-dna-concentration
Constraints: biosample-dna-concentration-nonnegative
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier SΣ 1..1 Identifier bio_sample_id – primary identifier for the biological sample
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
.... use ?!Σ 0..1 code usual | official | temp | secondary | old (If known)
Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .
.... type Σ 0..1 CodeableConcept Description of identifier
Binding: Identifier Type Codes (extensible): A coded type for an identifier that can be used to determine which identifier to use for a specific purpose.
.... system Σ 1..1 uri The namespace for the identifier value
Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/biosample-id
.... value Σ 1..1 string The value that is unique
Example General: 123456
.... period Σ 0..1 Period Time period when id is/was valid for use
.... assigner Σ 0..1 Reference(Organization) Organization that issued id (may be just text)
... 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 tissue_type – type of tissue sampled
Binding: BioSample Tissue Type ValueSet (required): The type of the specimen.
.... 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 1..1 string Plain text representation of the concept
... subject SΣ 1..1 Reference(Transplant Recipient) patient_id – reference to the transplant recipient
... receivedTime Σ 0..1 dateTime The time when specimen was received for processing
... parent 0..* Reference(Specimen) Specimen from which this specimen originated
... request 0..* Reference(ServiceRequest) Why the specimen was collected
... collection S 1..1 BackboneElement Sample collection details
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... collector Σ 0..1 Reference(Practitioner | PractitionerRole) Who collected the specimen
.... collected[x] Σ 1..1 dateTime collection_date – sample collection date
.... duration Σ 0..1 Duration How long it took to collect specimen
.... quantity 0..1 SimpleQuantity(4.0.1) The quantity of specimen collected
.... method 0..1 CodeableConcept Technique used to perform collection
Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.
.... bodySite 0..1 CodeableConcept Anatomical collection site
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
.... fastingStatus[x] Σ 0..1 Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.
..... fastingStatusCodeableConcept CodeableConcept
..... fastingStatusDuration Duration
... processing 0..* BackboneElement Processing and processing step details
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... description 0..1 string Textual description of procedure
.... procedure 0..1 CodeableConcept Indicates the treatment step applied to the specimen
Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen.
.... additive 0..* Reference(Substance) Material used in the processing step
.... time[x] 0..1 Date and time of specimen processing
..... timeDateTime dateTime
..... timePeriod Period
... container 0..* BackboneElement Direct container of specimen (tube/slide, etc.)
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... identifier Σ 0..* Identifier Id for the container
.... description 0..1 string Textual description of the container
.... type 0..1 CodeableConcept Kind of container directly associated with specimen
Binding: SpecimenContainerType (example): Type of specimen container.
.... capacity 0..1 SimpleQuantity(4.0.1) Container volume or size
.... specimenQuantity 0..1 SimpleQuantity(4.0.1) Quantity of specimen within container
.... additive[x] 0..1 Additive associated with container
Binding: hl7VS-additivePreservative (example): Substance added to specimen container.
..... additiveCodeableConcept CodeableConcept
..... additiveReference Reference(Substance)
... condition Σ 0..* CodeableConcept State of the specimen
Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.
... note 0..* Annotation Comments

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Specimen.language Base preferred Common Languages 📍4.0.1 FHIR Std.
Specimen.identifier.​use Base required IdentifierUse 📍4.0.1 FHIR Std.
Specimen.identifier.​type Base extensible IdentifierType 📍4.0.1 FHIR Std.
Specimen.status Base required SpecimenStatus 📍4.0.1 FHIR Std.
Specimen.type Base required BioSample Tissue Type ValueSet 📦0.1.0-ci-build This IG
Specimen.collection.​method Base example FHIR Specimen Collection Method 📍4.0.1 FHIR Std.
Specimen.collection.​bodySite Base example SNOMED CT Body Structures 📍4.0.1 FHIR Std.
Specimen.collection.​fastingStatus[x] Base extensible hl7VS-relevantClincialInformation 📦2.0.0 THO v7.0
Specimen.processing.​procedure Base example Specimen processing procedure 📍4.0.1 FHIR Std.
Specimen.container.type Base example Specimen Container Type 📍4.0.1 FHIR Std.
Specimen.container.additive[x] Base example hl7VS-additivePreservative 📦2.0.0 THO v7.0
Specimen.condition Base extensible hl7VS-specimenCondition 📦2.0.0 THO v7.0

Constraints

Id Grade Path(s) Description Expression
biosample-dna-concentration-nonnegative error Specimen.extension:dna_concentration DNA concentration must be zero or positive. valueDecimal >= 0
dom-2 error Specimen If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error 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 error 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 error Specimen If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Specimen A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen 0..* Specimen Sample for analysis
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:genomic_test_id S 0..1 Reference(Genomic Test) genomic_test_id – Reference to GenomicTest
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-genomic-test-ref
.... extension:epigenome_study_id S 0..1 Reference(Epigenome Study) epigenome_study_id – Reference to EpigenomeStudy
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-epigenome-study-ref
.... extension:methylomic_study_id S 0..1 Reference(Methylomic Study) methylomic_study_id – Reference to MethylomicStudy
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-methylomic-study-ref
.... extension:send_ingemm_date S 1..1 date send_ingemm_date – date sample sent to INGEMM
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-send-ingemm-date
.... extension:dna_concentration SC 0..1 decimal dna_concentration – DNA concentration (float, ≥ 0)
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-dna-concentration
Constraints: biosample-dna-concentration-nonnegative
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
.... use ?!Σ 0..1 code usual | official | temp | secondary | old (If known)
Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .
.... system Σ 1..1 uri The namespace for the identifier value
Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/biosample-id
.... value Σ 1..1 string The value that is unique
Example General: 123456
... 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 tissue_type – type of tissue sampled
Binding: BioSample Tissue Type ValueSet (required): The type of the specimen.
.... text Σ 1..1 string Plain text representation of the concept
... subject SΣ 1..1 Reference(Transplant Recipient) patient_id – reference to the transplant recipient
... collection S 1..1 BackboneElement Sample collection details
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... collected[x] Σ 1..1 dateTime collection_date – sample collection date

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Specimen.identifier.​use Base required IdentifierUse 📍4.0.1 FHIR Std.
Specimen.status Base required SpecimenStatus 📍4.0.1 FHIR Std.
Specimen.type Base required BioSample Tissue Type ValueSet 📦0.1.0-ci-build This IG

Constraints

Id Grade Path(s) Description Expression
biosample-dna-concentration-nonnegative error Specimen.extension:dna_concentration DNA concentration must be zero or positive. valueDecimal >= 0
dom-2 error Specimen If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error 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 error 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 error Specimen If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Specimen A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

Differential View

This structure is derived from Specimen

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen 0..* Specimen Sample for analysis
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:genomic_test_id S 0..1 Reference(Genomic Test) genomic_test_id – Reference to GenomicTest
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-genomic-test-ref
.... extension:epigenome_study_id S 0..1 Reference(Epigenome Study) epigenome_study_id – Reference to EpigenomeStudy
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-epigenome-study-ref
.... extension:methylomic_study_id S 0..1 Reference(Methylomic Study) methylomic_study_id – Reference to MethylomicStudy
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-methylomic-study-ref
.... extension:send_ingemm_date S 1..1 date send_ingemm_date – date sample sent to INGEMM
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-send-ingemm-date
.... extension:dna_concentration S 0..1 decimal dna_concentration – DNA concentration (float, ≥ 0)
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-dna-concentration
... identifier S 1..1 Identifier bio_sample_id – primary identifier for the biological sample
.... system 1..1 uri The namespace for the identifier value
Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/biosample-id
.... value 1..1 string The value that is unique
... type S 1..1 CodeableConcept tissue_type – type of tissue sampled
Binding: BioSample Tissue Type ValueSet (required): The type of the specimen.
.... text 1..1 string Plain text representation of the concept
... collection S 1..1 BackboneElement Sample collection details
.... collected[x] 1..1 dateTime collection_date – sample collection date

doco Documentation for this format

Terminology Bindings (Differential)

Path Status Usage ValueSet Version Source
Specimen.type Base required BioSample Tissue Type ValueSet 📦0.1.0-ci-build This IG

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. 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
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... Slices for extension 1..* Extension Extension
Slice: Unordered, Open by value:url
.... extension:genomic_test_id S 0..1 Reference(Genomic Test) genomic_test_id – Reference to GenomicTest
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-genomic-test-ref
.... extension:epigenome_study_id S 0..1 Reference(Epigenome Study) epigenome_study_id – Reference to EpigenomeStudy
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-epigenome-study-ref
.... extension:methylomic_study_id S 0..1 Reference(Methylomic Study) methylomic_study_id – Reference to MethylomicStudy
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-methylomic-study-ref
.... extension:send_ingemm_date S 1..1 date send_ingemm_date – date sample sent to INGEMM
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-send-ingemm-date
.... extension:dna_concentration SC 0..1 decimal dna_concentration – DNA concentration (float, ≥ 0)
URL: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/StructureDefinition/biosample-dna-concentration
Constraints: biosample-dna-concentration-nonnegative
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier SΣ 1..1 Identifier bio_sample_id – primary identifier for the biological sample
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
Slice: Unordered, Open by value:url
.... use ?!Σ 0..1 code usual | official | temp | secondary | old (If known)
Binding: IdentifierUse (required): Identifies the purpose for this identifier, if known .
.... type Σ 0..1 CodeableConcept Description of identifier
Binding: Identifier Type Codes (extensible): A coded type for an identifier that can be used to determine which identifier to use for a specific purpose.
.... system Σ 1..1 uri The namespace for the identifier value
Fixed Value: https://hl7.eu/fhir/ig/hl7.eu.fhir.protect-child/NamingSystem/biosample-id
.... value Σ 1..1 string The value that is unique
Example General: 123456
.... period Σ 0..1 Period Time period when id is/was valid for use
.... assigner Σ 0..1 Reference(Organization) Organization that issued id (may be just text)
... 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 tissue_type – type of tissue sampled
Binding: BioSample Tissue Type ValueSet (required): The type of the specimen.
.... 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 1..1 string Plain text representation of the concept
... subject SΣ 1..1 Reference(Transplant Recipient) patient_id – reference to the transplant recipient
... receivedTime Σ 0..1 dateTime The time when specimen was received for processing
... parent 0..* Reference(Specimen) Specimen from which this specimen originated
... request 0..* Reference(ServiceRequest) Why the specimen was collected
... collection S 1..1 BackboneElement Sample collection details
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... collector Σ 0..1 Reference(Practitioner | PractitionerRole) Who collected the specimen
.... collected[x] Σ 1..1 dateTime collection_date – sample collection date
.... duration Σ 0..1 Duration How long it took to collect specimen
.... quantity 0..1 SimpleQuantity(4.0.1) The quantity of specimen collected
.... method 0..1 CodeableConcept Technique used to perform collection
Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.
.... bodySite 0..1 CodeableConcept Anatomical collection site
Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
.... fastingStatus[x] Σ 0..1 Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.
..... fastingStatusCodeableConcept CodeableConcept
..... fastingStatusDuration Duration
... processing 0..* BackboneElement Processing and processing step details
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... description 0..1 string Textual description of procedure
.... procedure 0..1 CodeableConcept Indicates the treatment step applied to the specimen
Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen.
.... additive 0..* Reference(Substance) Material used in the processing step
.... time[x] 0..1 Date and time of specimen processing
..... timeDateTime dateTime
..... timePeriod Period
... container 0..* BackboneElement Direct container of specimen (tube/slide, etc.)
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... identifier Σ 0..* Identifier Id for the container
.... description 0..1 string Textual description of the container
.... type 0..1 CodeableConcept Kind of container directly associated with specimen
Binding: SpecimenContainerType (example): Type of specimen container.
.... capacity 0..1 SimpleQuantity(4.0.1) Container volume or size
.... specimenQuantity 0..1 SimpleQuantity(4.0.1) Quantity of specimen within container
.... additive[x] 0..1 Additive associated with container
Binding: hl7VS-additivePreservative (example): Substance added to specimen container.
..... additiveCodeableConcept CodeableConcept
..... additiveReference Reference(Substance)
... condition Σ 0..* CodeableConcept State of the specimen
Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.
... note 0..* Annotation Comments

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Specimen.language Base preferred Common Languages 📍4.0.1 FHIR Std.
Specimen.identifier.​use Base required IdentifierUse 📍4.0.1 FHIR Std.
Specimen.identifier.​type Base extensible IdentifierType 📍4.0.1 FHIR Std.
Specimen.status Base required SpecimenStatus 📍4.0.1 FHIR Std.
Specimen.type Base required BioSample Tissue Type ValueSet 📦0.1.0-ci-build This IG
Specimen.collection.​method Base example FHIR Specimen Collection Method 📍4.0.1 FHIR Std.
Specimen.collection.​bodySite Base example SNOMED CT Body Structures 📍4.0.1 FHIR Std.
Specimen.collection.​fastingStatus[x] Base extensible hl7VS-relevantClincialInformation 📦2.0.0 THO v7.0
Specimen.processing.​procedure Base example Specimen processing procedure 📍4.0.1 FHIR Std.
Specimen.container.type Base example Specimen Container Type 📍4.0.1 FHIR Std.
Specimen.container.additive[x] Base example hl7VS-additivePreservative 📦2.0.0 THO v7.0
Specimen.condition Base extensible hl7VS-specimenCondition 📦2.0.0 THO v7.0

Constraints

Id Grade Path(s) Description Expression
biosample-dna-concentration-nonnegative error Specimen.extension:dna_concentration DNA concentration must be zero or positive. valueDecimal >= 0
dom-2 error Specimen If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error 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 error 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 error Specimen If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Specimen A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

 

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