NCPI FHIR Implementation Guide v2 - Local Development build (v0.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

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Resource Profile: NCPI biospecimen definition for non-collected samples

NCPI biospecimen definition for non-collected samples

Usage:

• This Resource Profile is not used by any profiles in this Implementation Guide

Formal Views of Profile Content

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

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

This structure is derived from NCPISample

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	NCPISample	Sample for analysis
collection		0..0
Documentation for this format

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	NCPISample	Sample for analysis
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
Slices for extension				Content/Rules for all slices
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
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

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..*	NCPISample	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
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 NCPISample

Summary

Prohibited: 1 element

Differential View

This structure is derived from NCPISample

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	NCPISample	Sample for analysis
collection		0..0
Documentation for this format

Key Elements View

Name	Flags	Card.	Type	Description & Constraints
Specimen		0..*	NCPISample	Sample for analysis
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
Slices for extension				Content/Rules for all slices
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
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

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..*	NCPISample	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
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 NCPISample

Summary

Prohibited: 1 element

Other representations of profile: CSV, Excel, Schematron