Name	Flags	Card.	Type	Description & Constraints
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 for extension		0..*	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:sampleCollection	S	0..1	Identifier	Sample Collection URL: https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-collection-extension ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
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	Sample ID 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	Detailed Sample type Binding: DetailedSampleTypeVS (required) ele-1: All FHIR elements must have a @value or children
subject	SΣ	1..1	Reference(Sample Donor)	Donor of the 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 for collected[x]	Σ	0..1		Collection time Slice: Unordered, Open by type:$this ele-1: All FHIR elements must have a @value or children
collectedDateTime			dateTime
collectedPeriod			Period
collected[x]:collectedDateTime	SΣ	0..1	dateTime	Sample creation date and time ele-1: All FHIR elements must have a @value or children
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. ele-1: All FHIR elements must have a @value or children
coding	SΣC	0..1	Coding	Code defined by a terminology system ele-1: All FHIR elements must have a @value or children SpecimenOntologyInvariant: bodySite.concept.coding.system and bodySite.concept.coding.version are required if any ontology information is provided
system	Σ	0..1	uri	Identity of the terminology system ele-1: All FHIR elements must have a @value or children
version	Σ	0..1	string	Version of the system - if relevant ele-1: All FHIR elements must have a @value or children
code	Σ	0..1	code	Symbol in syntax defined by the system ele-1: All FHIR elements must have a @value or children
display	Σ	0..1	string	Representation defined by the system ele-1: All FHIR elements must have a @value or children
processing		0..*	BackboneElement	Processing and processing step details ele-1: All FHIR elements must have a @value or children
Slices for extension		0..*	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:storageTemperature	S	0..1	CodeableConcept	Sample storage temperature URL: https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-storage-temperature-extension Binding: Storage Temperature Value Set (required) ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
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
note	S	0..*	Annotation	Use restrictions ele-1: All FHIR elements must have a @value or children
text	SΣ	1..1	markdown	actual use restrictions ele-1: All FHIR elements must have a @value or children
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Specimen.status	required	SpecimenStatus http://hl7.org/fhir/ValueSet/specimen-status|4.0.1 from the FHIR Standard
Specimen.type	required	DetailedSampleTypeVS (a valid code from DetailedSampleType) https://fhir.bbmri-eric.eu/ValueSet/miabis-detailed-sample-type-vs from this IG
Specimen.collection.bodySite	example	SNOMEDCTBodyStructures http://hl7.org/fhir/ValueSet/body-site from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
SpecimenOntologyInvariant	error	Specimen.collection.bodySite.coding	bodySite.concept.coding.system and bodySite.concept.coding.version are required if any ontology information is provided : Specimen.collection.bodySite.concept.coding.exists() implies (Specimen.collection.bodySite.concept.coding.system.exists() and Specimen.collection.bodySite.concept.coding.version.exists())
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()

Name	Flags	Card.	Type	Description & Constraints
Specimen			Specimen
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:sampleCollection	S	0..1	Identifier	Sample Collection URL: https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-collection-extension
identifier	S	1..1	Identifier	Sample ID
type	S	1..1	CodeableConcept	Detailed Sample type Binding: DetailedSampleTypeVS (required)
subject	S	1..1	Reference(Sample Donor)	Donor of the sample
collection
Slices for collected[x]		0..1	dateTime, Period	Collection time Slice: Unordered, Open by type:$this
collected[x]:collectedDateTime	S	0..1	dateTime	Sample creation date and time
bodySite
coding	SC	0..1	Coding	Code defined by a terminology system SpecimenOntologyInvariant: bodySite.concept.coding.system and bodySite.concept.coding.version are required if any ontology information is provided
system		0..1	uri	Identity of the terminology system
version		0..1	string	Version of the system - if relevant
code		0..1	code	Symbol in syntax defined by the system
display		0..1	string	Representation defined by the system
processing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:storageTemperature	S	0..1	CodeableConcept	Sample storage temperature URL: https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-storage-temperature-extension Binding: Storage Temperature Value Set (required)
note	S	0..*	Annotation	Use restrictions
text	S	1..1	markdown	actual use restrictions
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet	URI
Specimen.type	required	DetailedSampleTypeVS (a valid code from DetailedSampleType) https://fhir.bbmri-eric.eu/ValueSet/miabis-detailed-sample-type-vs from this IG

Constraints

Id	Grade	Path(s)	Details	Requirements
SpecimenOntologyInvariant	error	Specimen.collection.bodySite.coding	bodySite.concept.coding.system and bodySite.concept.coding.version are required if any ontology information is provided : Specimen.collection.bodySite.concept.coding.exists() implies (Specimen.collection.bodySite.concept.coding.system.exists() and Specimen.collection.bodySite.concept.coding.version.exists())

Name	Flags	Card.	Type	Description & Constraints
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. Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:sampleCollection	S	0..1	Identifier	Sample Collection URL: https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-collection-extension
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	SΣ	1..1	Identifier	Sample ID
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	Detailed Sample type Binding: DetailedSampleTypeVS (required)
subject	SΣ	1..1	Reference(Sample Donor)	Donor of the sample
receivedTime	Σ	0..1	dateTime	The time when specimen was received for processing
parent		0..*	Reference(Specimen)	Specimen from which this specimen originated
request		0..*	Reference(ServiceRequest)	Why the specimen was collected
collection		0..1	BackboneElement	Collection details
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
collector	Σ	0..1	Reference(Practitioner | PractitionerRole)	Who collected the specimen
Slices for collected[x]	Σ	0..1		Collection time Slice: Unordered, Open by type:$this
collectedDateTime			dateTime
collectedPeriod			Period
collected[x]:collectedDateTime	SΣ	0..1	dateTime	Sample creation date and time
duration	Σ	0..1	Duration	How long it took to collect specimen
quantity		0..1	SimpleQuantity	The quantity of specimen collected
method		0..1	CodeableConcept	Technique used to perform collection Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
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	SΣC	0..1	Coding	Code defined by a terminology system SpecimenOntologyInvariant: bodySite.concept.coding.system and bodySite.concept.coding.version are required if any ontology information is provided
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
system	Σ	0..1	uri	Identity of the terminology system
version	Σ	0..1	string	Version of the system - if relevant
code	Σ	0..1	code	Symbol in syntax defined by the system
display	Σ	0..1	string	Representation defined by the system
userSelected	Σ	0..1	boolean	If this coding was chosen directly by the user
text	Σ	0..1	string	Plain text representation of the concept
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
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:storageTemperature	S	0..1	CodeableConcept	Sample storage temperature URL: https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-storage-temperature-extension Binding: Storage Temperature Value Set (required)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
description		0..1	string	Textual description of procedure
procedure		0..1	CodeableConcept	Indicates the treatment step applied to the specimen Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen.
additive		0..*	Reference(Substance)	Material used in the processing step
time[x]		0..1		Date and time of specimen processing
timeDateTime			dateTime
timePeriod			Period
container		0..*	BackboneElement	Direct container of specimen (tube/slide, etc.)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
identifier	Σ	0..*	Identifier	Id for the container
description		0..1	string	Textual description of the container
type		0..1	CodeableConcept	Kind of container directly associated with specimen Binding: SpecimenContainerType (example): Type of specimen container.
capacity		0..1	SimpleQuantity	Container volume or size
specimenQuantity		0..1	SimpleQuantity	Quantity of specimen within container
additive[x]		0..1		Additive associated with container Binding: hl7VS-additivePreservative (example): Substance added to specimen container.
additiveCodeableConcept			CodeableConcept
additiveReference			Reference(Substance)
condition	Σ	0..*	CodeableConcept	State of the specimen Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.
note	S	0..*	Annotation	Use restrictions
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
author[x]	Σ	0..1		Individual responsible for the annotation
authorReference			Reference(Practitioner | Patient | RelatedPerson | Organization)
authorString			string
time	Σ	0..1	dateTime	When the annotation was made
text	SΣ	1..1	markdown	actual use restrictions
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Specimen.language	preferred	CommonLanguages http://hl7.org/fhir/ValueSet/languages from the FHIR Standard Additional Bindings Purpose AllLanguages Max Binding
Specimen.status	required	SpecimenStatus http://hl7.org/fhir/ValueSet/specimen-status|4.0.1 from the FHIR Standard
Specimen.type	required	DetailedSampleTypeVS (a valid code from DetailedSampleType) https://fhir.bbmri-eric.eu/ValueSet/miabis-detailed-sample-type-vs from this IG
Specimen.collection.method	example	FHIRSpecimenCollectionMethod http://hl7.org/fhir/ValueSet/specimen-collection-method from the FHIR Standard
Specimen.collection.bodySite	example	SNOMEDCTBodyStructures http://hl7.org/fhir/ValueSet/body-site from the FHIR Standard
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	Hl7VSSpecimenCondition http://terminology.hl7.org/ValueSet/v2-0493

Constraints

Id	Grade	Path(s)	Details	Requirements
SpecimenOntologyInvariant	error	Specimen.collection.bodySite.coding	bodySite.concept.coding.system and bodySite.concept.coding.version are required if any ontology information is provided : Specimen.collection.bodySite.concept.coding.exists() implies (Specimen.collection.bodySite.concept.coding.system.exists() and Specimen.collection.bodySite.concept.coding.version.exists())
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()

Summary

Mandatory: 3 elements
Must-Support: 9 elements

Structures

This structure refers to these other structures:

• Sample Donor (https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-donor)

Extensions

This structure refers to these extensions:

• https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-collection-extension
• https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-storage-temperature-extension

Slices

This structure defines the following Slices:

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

Name	Flags	Card.	Type	Description & Constraints
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 for extension		0..*	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:sampleCollection	S	0..1	Identifier	Sample Collection URL: https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-collection-extension ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
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	Sample ID 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	Detailed Sample type Binding: DetailedSampleTypeVS (required) ele-1: All FHIR elements must have a @value or children
subject	SΣ	1..1	Reference(Sample Donor)	Donor of the 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 for collected[x]	Σ	0..1		Collection time Slice: Unordered, Open by type:$this ele-1: All FHIR elements must have a @value or children
collectedDateTime			dateTime
collectedPeriod			Period
collected[x]:collectedDateTime	SΣ	0..1	dateTime	Sample creation date and time ele-1: All FHIR elements must have a @value or children
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality. ele-1: All FHIR elements must have a @value or children
coding	SΣC	0..1	Coding	Code defined by a terminology system ele-1: All FHIR elements must have a @value or children SpecimenOntologyInvariant: bodySite.concept.coding.system and bodySite.concept.coding.version are required if any ontology information is provided
system	Σ	0..1	uri	Identity of the terminology system ele-1: All FHIR elements must have a @value or children
version	Σ	0..1	string	Version of the system - if relevant ele-1: All FHIR elements must have a @value or children
code	Σ	0..1	code	Symbol in syntax defined by the system ele-1: All FHIR elements must have a @value or children
display	Σ	0..1	string	Representation defined by the system ele-1: All FHIR elements must have a @value or children
processing		0..*	BackboneElement	Processing and processing step details ele-1: All FHIR elements must have a @value or children
Slices for extension		0..*	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:storageTemperature	S	0..1	CodeableConcept	Sample storage temperature URL: https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-storage-temperature-extension Binding: Storage Temperature Value Set (required) ele-1: All FHIR elements must have a @value or children ext-1: Must have either extensions or value[x], not both
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
note	S	0..*	Annotation	Use restrictions ele-1: All FHIR elements must have a @value or children
text	SΣ	1..1	markdown	actual use restrictions ele-1: All FHIR elements must have a @value or children
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Specimen.status	required	SpecimenStatus http://hl7.org/fhir/ValueSet/specimen-status|4.0.1 from the FHIR Standard
Specimen.type	required	DetailedSampleTypeVS (a valid code from DetailedSampleType) https://fhir.bbmri-eric.eu/ValueSet/miabis-detailed-sample-type-vs from this IG
Specimen.collection.bodySite	example	SNOMEDCTBodyStructures http://hl7.org/fhir/ValueSet/body-site from the FHIR Standard

Constraints

Id	Grade	Path(s)	Details	Requirements
SpecimenOntologyInvariant	error	Specimen.collection.bodySite.coding	bodySite.concept.coding.system and bodySite.concept.coding.version are required if any ontology information is provided : Specimen.collection.bodySite.concept.coding.exists() implies (Specimen.collection.bodySite.concept.coding.system.exists() and Specimen.collection.bodySite.concept.coding.version.exists())
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()

Name	Flags	Card.	Type	Description & Constraints
Specimen			Specimen
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:sampleCollection	S	0..1	Identifier	Sample Collection URL: https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-collection-extension
identifier	S	1..1	Identifier	Sample ID
type	S	1..1	CodeableConcept	Detailed Sample type Binding: DetailedSampleTypeVS (required)
subject	S	1..1	Reference(Sample Donor)	Donor of the sample
collection
Slices for collected[x]		0..1	dateTime, Period	Collection time Slice: Unordered, Open by type:$this
collected[x]:collectedDateTime	S	0..1	dateTime	Sample creation date and time
bodySite
coding	SC	0..1	Coding	Code defined by a terminology system SpecimenOntologyInvariant: bodySite.concept.coding.system and bodySite.concept.coding.version are required if any ontology information is provided
system		0..1	uri	Identity of the terminology system
version		0..1	string	Version of the system - if relevant
code		0..1	code	Symbol in syntax defined by the system
display		0..1	string	Representation defined by the system
processing
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:storageTemperature	S	0..1	CodeableConcept	Sample storage temperature URL: https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-storage-temperature-extension Binding: Storage Temperature Value Set (required)
note	S	0..*	Annotation	Use restrictions
text	S	1..1	markdown	actual use restrictions
Documentation for this format

Terminology Bindings (Differential)

Path	Conformance	ValueSet	URI
Specimen.type	required	DetailedSampleTypeVS (a valid code from DetailedSampleType) https://fhir.bbmri-eric.eu/ValueSet/miabis-detailed-sample-type-vs from this IG

Constraints

Id	Grade	Path(s)	Details	Requirements
SpecimenOntologyInvariant	error	Specimen.collection.bodySite.coding	bodySite.concept.coding.system and bodySite.concept.coding.version are required if any ontology information is provided : Specimen.collection.bodySite.concept.coding.exists() implies (Specimen.collection.bodySite.concept.coding.system.exists() and Specimen.collection.bodySite.concept.coding.version.exists())

Name	Flags	Card.	Type	Description & Constraints
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. Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:sampleCollection	S	0..1	Identifier	Sample Collection URL: https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-collection-extension
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	SΣ	1..1	Identifier	Sample ID
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	Detailed Sample type Binding: DetailedSampleTypeVS (required)
subject	SΣ	1..1	Reference(Sample Donor)	Donor of the sample
receivedTime	Σ	0..1	dateTime	The time when specimen was received for processing
parent		0..*	Reference(Specimen)	Specimen from which this specimen originated
request		0..*	Reference(ServiceRequest)	Why the specimen was collected
collection		0..1	BackboneElement	Collection details
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
collector	Σ	0..1	Reference(Practitioner | PractitionerRole)	Who collected the specimen
Slices for collected[x]	Σ	0..1		Collection time Slice: Unordered, Open by type:$this
collectedDateTime			dateTime
collectedPeriod			Period
collected[x]:collectedDateTime	SΣ	0..1	dateTime	Sample creation date and time
duration	Σ	0..1	Duration	How long it took to collect specimen
quantity		0..1	SimpleQuantity	The quantity of specimen collected
method		0..1	CodeableConcept	Technique used to perform collection Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.
bodySite		0..1	CodeableConcept	Anatomical collection site Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
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	SΣC	0..1	Coding	Code defined by a terminology system SpecimenOntologyInvariant: bodySite.concept.coding.system and bodySite.concept.coding.version are required if any ontology information is provided
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
system	Σ	0..1	uri	Identity of the terminology system
version	Σ	0..1	string	Version of the system - if relevant
code	Σ	0..1	code	Symbol in syntax defined by the system
display	Σ	0..1	string	Representation defined by the system
userSelected	Σ	0..1	boolean	If this coding was chosen directly by the user
text	Σ	0..1	string	Plain text representation of the concept
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
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:storageTemperature	S	0..1	CodeableConcept	Sample storage temperature URL: https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-storage-temperature-extension Binding: Storage Temperature Value Set (required)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
description		0..1	string	Textual description of procedure
procedure		0..1	CodeableConcept	Indicates the treatment step applied to the specimen Binding: SpecimenProcessingProcedure (example): Type indicating the technique used to process the specimen.
additive		0..*	Reference(Substance)	Material used in the processing step
time[x]		0..1		Date and time of specimen processing
timeDateTime			dateTime
timePeriod			Period
container		0..*	BackboneElement	Direct container of specimen (tube/slide, etc.)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
identifier	Σ	0..*	Identifier	Id for the container
description		0..1	string	Textual description of the container
type		0..1	CodeableConcept	Kind of container directly associated with specimen Binding: SpecimenContainerType (example): Type of specimen container.
capacity		0..1	SimpleQuantity	Container volume or size
specimenQuantity		0..1	SimpleQuantity	Quantity of specimen within container
additive[x]		0..1		Additive associated with container Binding: hl7VS-additivePreservative (example): Substance added to specimen container.
additiveCodeableConcept			CodeableConcept
additiveReference			Reference(Substance)
condition	Σ	0..*	CodeableConcept	State of the specimen Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.
note	S	0..*	Annotation	Use restrictions
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
author[x]	Σ	0..1		Individual responsible for the annotation
authorReference			Reference(Practitioner | Patient | RelatedPerson | Organization)
authorString			string
time	Σ	0..1	dateTime	When the annotation was made
text	SΣ	1..1	markdown	actual use restrictions
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Specimen.language	preferred	CommonLanguages http://hl7.org/fhir/ValueSet/languages from the FHIR Standard Additional Bindings Purpose AllLanguages Max Binding
Specimen.status	required	SpecimenStatus http://hl7.org/fhir/ValueSet/specimen-status|4.0.1 from the FHIR Standard
Specimen.type	required	DetailedSampleTypeVS (a valid code from DetailedSampleType) https://fhir.bbmri-eric.eu/ValueSet/miabis-detailed-sample-type-vs from this IG
Specimen.collection.method	example	FHIRSpecimenCollectionMethod http://hl7.org/fhir/ValueSet/specimen-collection-method from the FHIR Standard
Specimen.collection.bodySite	example	SNOMEDCTBodyStructures http://hl7.org/fhir/ValueSet/body-site from the FHIR Standard
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	Hl7VSSpecimenCondition http://terminology.hl7.org/ValueSet/v2-0493

Constraints

Id	Grade	Path(s)	Details	Requirements
SpecimenOntologyInvariant	error	Specimen.collection.bodySite.coding	bodySite.concept.coding.system and bodySite.concept.coding.version are required if any ontology information is provided : Specimen.collection.bodySite.concept.coding.exists() implies (Specimen.collection.bodySite.concept.coding.system.exists() and Specimen.collection.bodySite.concept.coding.version.exists())
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()

Summary

Mandatory: 3 elements
Must-Support: 9 elements

Structures

This structure refers to these other structures:

• Sample Donor (https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-donor)

Extensions

This structure refers to these extensions:

• https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-collection-extension
• https://fhir.bbmri-eric.eu/StructureDefinition/miabis-sample-storage-temperature-extension

Slices

This structure defines the following Slices:

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