Basic Definition

The collection element allows for high level organization of objects into various related groups. One common type of collection is a consortium, but other collections can also be established. Items in a collection can include studies, datasets, or other collections (for example, if consortium A becomes a member of consortium B, the collection that represents consortium A can be added as an item in the collection representing consortium B).

Primary Profile Restrictions and Enhancements

• title must be defined in order for users to understand the purpose of the collection.
• code must be defined and should be one of the codes from the CodeSystem, CollectionType, when possible.
• note should contain a meaningful description whenever possible.
• there must be one or more entries referencing the "contained" resources.
• When possible, a website should be provided. For Consortium, programs and other entities with formal websites, this should be the one that provides the best overview of the group. For adhoc collections, or those collections that are less formally defined, an online document may be sufficient.

Key Guidelines

The NCPI Sample profile is based on the standard resource type, Specimen and encompasses biospecimen collection, sample information, and aliquot information.

Added Profile Restrictions

Recommended Practices

• The NCPI Sample profile is broken up into "NCPI Collected Sample" and "NCPI Non-collected Sample".

TODO: continue recommended practices

FHIR Mappings

The following fields from the shared data model are to be mapped into the NCPI Biospecimen as follows:

Biospecimen Collection:

Sample:

Aliquot:

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

This structure is derived from Specimen

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
biospecimen-spatial		0..1	code	Any spatial/location qualifiers URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
biospecimen-laterality		0..1	code	Laterality information for the site URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
aliquot-availability		0..1	code	Can this Sample be requested for further analysis? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
aliquot-concentration		0..1	Quantity	What is the concentration of the analyte in the Aliquot? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-concentration
identifier		1..1	Identifier	Unique ID for this sample
status		0..1	code	Can this Sample be requested for further analysis?
type		1..1	CodeableConcept	The type of material of which this Sample is comprised
subject		1..1	Reference(Patient | Group | Device | Substance | Location)	The participant from whom the biospecimen was taken
parent		0..*	Reference(Specimen)	The Sample from which this Sample was derived
collection
collected[x]		0..1	dateTime	The age at which this biospecimen was collected. Could be expressed with a term, an age, or an age range. (for ages use http://hl7.org/fhir/StructureDefinition/cqf-relativeDateTime)
quantity		0..1	SimpleQuantity	The total quantity of the specimen
method		0..1	CodeableConcept	The approach used to collect the biospecimen
bodySite		0..1	CodeableConcept	The location of the specimen collection
processing
procedure		1..1	CodeableConcept	Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample
container
identifier		1..1	Identifier	Unique ID for this aliquot
specimenQuantity		0..1	SimpleQuantity	What is the volume of the Aliquot?
condition		0..*	CodeableConcept	How is the Sample stored, eg, Frozen or with additives
Documentation for this format

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
biospecimen-spatial		0..1	code	Any spatial/location qualifiers URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
biospecimen-laterality		0..1	code	Laterality information for the site URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
aliquot-availability		0..1	code	Can this Sample be requested for further analysis? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
aliquot-concentration		0..1	Quantity	What is the concentration of the analyte in the Aliquot? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-concentration
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	1..1	Identifier	Unique ID for this sample
status	?!Σ	0..1	code	Can this Sample be requested for further analysis? Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
type	Σ	1..1	CodeableConcept	The type of material of which this Sample is comprised Binding: hl7VS-specimenType (example): The type of the specimen.
subject	Σ	1..1	Reference(Patient | Group | Device | Substance | Location)	The participant from whom the biospecimen was taken
parent		0..*	Reference(Specimen)	The Sample from which this Sample was derived
condition	Σ	0..*	CodeableConcept	How is the Sample stored, eg, Frozen or with additives Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Specimen.status	required	SpecimenStatus http://hl7.org/fhir/ValueSet/specimen-status|4.3.0 from the FHIR Standard
Specimen.type	example	Hl7VSSpecimenType http://terminology.hl7.org/ValueSet/v2-0487
Specimen.condition	extensible	Hl7VSSpecimenCondition http://terminology.hl7.org/ValueSet/v2-0493

Constraints

Id	Grade	Path(s)	Details	Requirements
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.exists() and ('#'+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(uri) = '#').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		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): IETF language tag Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources dom-r4b: Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
biospecimen-spatial		0..1	code	Any spatial/location qualifiers URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
biospecimen-laterality		0..1	code	Laterality information for the site URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
aliquot-availability		0..1	code	Can this Sample be requested for further analysis? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
aliquot-concentration		0..1	Quantity	What is the concentration of the analyte in the Aliquot? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-concentration
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	1..1	Identifier	Unique ID for this sample
accessionIdentifier	Σ	0..1	Identifier	Identifier assigned by the lab
status	?!Σ	0..1	code	Can this Sample be requested for further analysis? Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
type	Σ	1..1	CodeableConcept	The type of material of which this Sample is comprised Binding: hl7VS-specimenType (example): The type of the specimen.
subject	Σ	1..1	Reference(Patient | Group | Device | Substance | Location)	The participant from whom the biospecimen was taken
receivedTime	Σ	0..1	dateTime	The time when specimen was received for processing
parent		0..*	Reference(Specimen)	The Sample from which this Sample was derived
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
collected[x]	Σ	0..1	dateTime	The age at which this biospecimen was collected. Could be expressed with a term, an age, or an age range. (for ages use http://hl7.org/fhir/StructureDefinition/cqf-relativeDateTime)
duration	Σ	0..1	Duration	How long it took to collect specimen
quantity		0..1	SimpleQuantity	The total quantity of the specimen
method		0..1	CodeableConcept	The approach used to collect the biospecimen Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.
bodySite		0..1	CodeableConcept	The location of the specimen collection Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts
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		1..1	CodeableConcept	Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample 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	1..1	Identifier	Unique ID for this aliquot
description		0..1	string	Textual description of the container
type		0..1	CodeableConcept	Kind of container directly associated with specimen Binding: SpecimenContainer (example): Type of specimen container.
capacity		0..1	SimpleQuantity	Container volume or size
specimenQuantity		0..1	SimpleQuantity	What is the volume of the Aliquot?
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	How is the Sample stored, eg, Frozen or with additives Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.
note		0..*	Annotation	Comments
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Specimen.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding http://hl7.org/fhir/ValueSet/languages from the FHIR Standard
Specimen.status	required	SpecimenStatus http://hl7.org/fhir/ValueSet/specimen-status|4.3.0 from the FHIR Standard
Specimen.type	example	Hl7VSSpecimenType http://terminology.hl7.org/ValueSet/v2-0487
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	SpecimenContainer 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
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.exists() and ('#'+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(uri) = '#').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()
dom-r4b	warning	Specimen.contained	Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems : ($this is Citation or $this is Evidence or $this is EvidenceReport or $this is EvidenceVariable or $this is MedicinalProductDefinition or $this is PackagedProductDefinition or $this is AdministrableProductDefinition or $this is Ingredient or $this is ClinicalUseDefinition or $this is RegulatedAuthorization or $this is SubstanceDefinition or $this is SubscriptionStatus or $this is SubscriptionTopic) implies (%resource is Citation or %resource is Evidence or %resource is EvidenceReport or %resource is EvidenceVariable or %resource is MedicinalProductDefinition or %resource is PackagedProductDefinition or %resource is AdministrableProductDefinition or %resource is Ingredient or %resource is ClinicalUseDefinition or %resource is RegulatedAuthorization or %resource is SubstanceDefinition or %resource is SubscriptionStatus or %resource is SubscriptionTopic)
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

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
biospecimen-spatial		0..1	code	Any spatial/location qualifiers URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
biospecimen-laterality		0..1	code	Laterality information for the site URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
aliquot-availability		0..1	code	Can this Sample be requested for further analysis? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
aliquot-concentration		0..1	Quantity	What is the concentration of the analyte in the Aliquot? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-concentration
identifier		1..1	Identifier	Unique ID for this sample
status		0..1	code	Can this Sample be requested for further analysis?
type		1..1	CodeableConcept	The type of material of which this Sample is comprised
subject		1..1	Reference(Patient | Group | Device | Substance | Location)	The participant from whom the biospecimen was taken
parent		0..*	Reference(Specimen)	The Sample from which this Sample was derived
collection
collected[x]		0..1	dateTime	The age at which this biospecimen was collected. Could be expressed with a term, an age, or an age range. (for ages use http://hl7.org/fhir/StructureDefinition/cqf-relativeDateTime)
quantity		0..1	SimpleQuantity	The total quantity of the specimen
method		0..1	CodeableConcept	The approach used to collect the biospecimen
bodySite		0..1	CodeableConcept	The location of the specimen collection
processing
procedure		1..1	CodeableConcept	Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample
container
identifier		1..1	Identifier	Unique ID for this aliquot
specimenQuantity		0..1	SimpleQuantity	What is the volume of the Aliquot?
condition		0..*	CodeableConcept	How is the Sample stored, eg, Frozen or with additives
Documentation for this format

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	Specimen	Sample for analysis
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
biospecimen-spatial		0..1	code	Any spatial/location qualifiers URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
biospecimen-laterality		0..1	code	Laterality information for the site URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
aliquot-availability		0..1	code	Can this Sample be requested for further analysis? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
aliquot-concentration		0..1	Quantity	What is the concentration of the analyte in the Aliquot? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-concentration
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	1..1	Identifier	Unique ID for this sample
status	?!Σ	0..1	code	Can this Sample be requested for further analysis? Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
type	Σ	1..1	CodeableConcept	The type of material of which this Sample is comprised Binding: hl7VS-specimenType (example): The type of the specimen.
subject	Σ	1..1	Reference(Patient | Group | Device | Substance | Location)	The participant from whom the biospecimen was taken
parent		0..*	Reference(Specimen)	The Sample from which this Sample was derived
condition	Σ	0..*	CodeableConcept	How is the Sample stored, eg, Frozen or with additives Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Specimen.status	required	SpecimenStatus http://hl7.org/fhir/ValueSet/specimen-status|4.3.0 from the FHIR Standard
Specimen.type	example	Hl7VSSpecimenType http://terminology.hl7.org/ValueSet/v2-0487
Specimen.condition	extensible	Hl7VSSpecimenCondition http://terminology.hl7.org/ValueSet/v2-0493

Constraints

Id	Grade	Path(s)	Details	Requirements
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.exists() and ('#'+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(uri) = '#').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()

Snapshot View

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): IETF language tag Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation
contained		0..*	Resource	Contained, inline Resources dom-r4b: Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
biospecimen-spatial		0..1	code	Any spatial/location qualifiers URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
biospecimen-laterality		0..1	code	Laterality information for the site URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
aliquot-availability		0..1	code	Can this Sample be requested for further analysis? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
aliquot-concentration		0..1	Quantity	What is the concentration of the analyte in the Aliquot? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-concentration
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	1..1	Identifier	Unique ID for this sample
accessionIdentifier	Σ	0..1	Identifier	Identifier assigned by the lab
status	?!Σ	0..1	code	Can this Sample be requested for further analysis? Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen.
type	Σ	1..1	CodeableConcept	The type of material of which this Sample is comprised Binding: hl7VS-specimenType (example): The type of the specimen.
subject	Σ	1..1	Reference(Patient | Group | Device | Substance | Location)	The participant from whom the biospecimen was taken
receivedTime	Σ	0..1	dateTime	The time when specimen was received for processing
parent		0..*	Reference(Specimen)	The Sample from which this Sample was derived
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
collected[x]	Σ	0..1	dateTime	The age at which this biospecimen was collected. Could be expressed with a term, an age, or an age range. (for ages use http://hl7.org/fhir/StructureDefinition/cqf-relativeDateTime)
duration	Σ	0..1	Duration	How long it took to collect specimen
quantity		0..1	SimpleQuantity	The total quantity of the specimen
method		0..1	CodeableConcept	The approach used to collect the biospecimen Binding: FHIRSpecimenCollectionMethod (example): The technique that is used to perform the procedure.
bodySite		0..1	CodeableConcept	The location of the specimen collection Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts
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		1..1	CodeableConcept	Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample 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	1..1	Identifier	Unique ID for this aliquot
description		0..1	string	Textual description of the container
type		0..1	CodeableConcept	Kind of container directly associated with specimen Binding: SpecimenContainer (example): Type of specimen container.
capacity		0..1	SimpleQuantity	Container volume or size
specimenQuantity		0..1	SimpleQuantity	What is the volume of the Aliquot?
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	How is the Sample stored, eg, Frozen or with additives Binding: hl7VS-specimenCondition (extensible): Codes describing the state of the specimen.
note		0..*	Annotation	Comments
Documentation for this format

Terminology Bindings

Path	Conformance	ValueSet	URI
Specimen.language	preferred	CommonLanguages Additional Bindings Purpose AllLanguages Max Binding http://hl7.org/fhir/ValueSet/languages from the FHIR Standard
Specimen.status	required	SpecimenStatus http://hl7.org/fhir/ValueSet/specimen-status|4.3.0 from the FHIR Standard
Specimen.type	example	Hl7VSSpecimenType http://terminology.hl7.org/ValueSet/v2-0487
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	SpecimenContainer 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
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.exists() and ('#'+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(uri) = '#').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()
dom-r4b	warning	Specimen.contained	Containing new R4B resources within R4 resources may cause interoperability issues if instances are shared with R4 systems : ($this is Citation or $this is Evidence or $this is EvidenceReport or $this is EvidenceVariable or $this is MedicinalProductDefinition or $this is PackagedProductDefinition or $this is AdministrableProductDefinition or $this is Ingredient or $this is ClinicalUseDefinition or $this is RegulatedAuthorization or $this is SubstanceDefinition or $this is SubscriptionStatus or $this is SubscriptionTopic) implies (%resource is Citation or %resource is Evidence or %resource is EvidenceReport or %resource is EvidenceVariable or %resource is MedicinalProductDefinition or %resource is PackagedProductDefinition or %resource is AdministrableProductDefinition or %resource is Ingredient or %resource is ClinicalUseDefinition or %resource is RegulatedAuthorization or %resource is SubstanceDefinition or %resource is SubscriptionStatus or %resource is SubscriptionTopic)
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

Summary

Mandatory: 3 elements(2 nested mandatory elements)

Extensions

This structure refers to these extensions:

• https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
• https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
• https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
• https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-concentration