NCPI FHIR Implementation Guide v2
0.2.0 - ci-build

NCPI FHIR Implementation Guide v2 - Local Development build (v0.2.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Resource Profile: NCPI Sample

Official URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-sample Version: 0.2.0
Draft as of 2025-12-03 Computable Name: NCPISample

FHIR Profile for NCPI Sample

Basic Information

Key Guidelines

The NCPI Sample profile is based on the standard resource type, Specimen and encompasses biospecimen collection, sample information, and aliquot information. Biospecimen collection information can be excluded if unavailable. However, if there is no parent sample, collection information must be included, even if the value is unknown.

Added Profile Restrictions
  • There are 3 Unique Identifiers in the collected sample profile: one for Biospecimen Collection, Sample, and Aliquot, respectively. These IDs are different than the participant from whom this sample was derived.
  • The NCPI Sample profile includes collection information. If this data is unavailable, you should set collection method to "unknown".
FHIR Mappings

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

Biospecimen Collection:

Logical Model Property Cardinality NCPI Sample Mapping Usage Guidance Notes
sampleGenerated 1..1 MISSING Sample that was generated from this collection event  
participant 1..1 subject The participant from whom the biospecimen was taken  
ageAtCollection 0..1 collection.collected The age at which this biospecimen was collected. Could be expressed with a term, an age, or an age range.  
method 0..1 collection.method The approach used to collect the biospecimen Recommended to use LOINC
site 0..1 collection.bodySite The location of the specimen collection  
spatial 0..1 extension[biospecimen-spatial] Any spatial/location qualifiers URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
laterality 0..1 extension[biospecimen-laterality] Laterality information for the site URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality

Sample:

Logical Model Property Cardinality NCPI Sample Mapping Usage Guidance Notes
sampleId 1..1 identifier Unique ID for this sample  
participant 1..1 subject The participant from whom the biospecimen was taken  
parentSample 0..* parent The Sample from which this Sample was derived  
type 1..1 type The type of material of which this Sample is comprised  
processing 0..* processing Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample  
availabilityStatus 0..1 status Can this Sample be requested for further analysis? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
storageMethod 0..1 collection.method The approach used to collect the biospecimen Recommended to use Hl7VSSpecimenCondition
quantity 0..1 collection.quantity The total quantity of the specimen  

Aliquot:

Logical Model Property Cardinality NCPI Sample Mapping Usage Guidance Notes
aliquotId 1..1 container.identifier Unique ID for this aliquot  
sample 1..1 MISSING The sample of which this tube is a part.  
availabilityStatus 0..1 extension[aliquot-availability] Can this Sample be requested for further analysis? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
volume 0..1 container.specimenQuantity What is the volume of the Aliquot?  
concentration 0..1 extension[aliquot-concentration] What is the concentration of the analyte in the Aliquot? URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-concentration

Usages:

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

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

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen C 0..* Specimen Sample for analysis
Constraints: collection-xor-parent
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Unique ID for this sample
... 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
... collection 0..1 BackboneElement Information about how the biospecimen was collected. Collection information may be unknown, but must be included when there is no parent sample
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:biospecimenSpatial 0..1 code Any spatial/location qualifiers
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
..... extension:biospecimenLaterality 0..1 code Laterality information for the site
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... 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)
.... quantity 0..1 SimpleQuantity(4.0.1) The total quantity of the specimen
.... method 0..1 CodeableConcept The approach used to collect the biospecimen (unknown if not provided)
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): Codes describing anatomical locations. May include laterality.
... 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.

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Specimen.status Base required SpecimenStatus 📍4.0.1 FHIR Std.
Specimen.type Base example hl7VS-specimenType 📦2.0.0 THO v7.0
Specimen.collection.​method Base example FHIR Specimen Collection Method 📍4.0.1 FHIR Std.
Specimen.collection.​bodySite Base example SNOMED CT Body Structures 📍4.0.1 FHIR Std.
Specimen.condition Base extensible hl7VS-specimenCondition 📦2.0.0 THO v7.0

Constraints

Id Grade Path(s) Description Expression
collection-xor-parent warning Specimen If there is a parent sample, there should be no collection information. If there is collection information present, there should be no parent sample. parent.exists().not() or collection.exists().not()
dom-2 error Specimen If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Specimen If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Specimen If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Specimen If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Specimen A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

This structure is derived from Specimen

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen C 0..* Specimen Sample for analysis
Constraints: collection-xor-parent
... identifier 0..* 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
... parent 0..* Reference(Specimen) The Sample from which this Sample was derived
... collection 0..1 BackboneElement Information about how the biospecimen was collected. Collection information may be unknown, but must be included when there is no parent sample
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:biospecimenSpatial 0..1 code Any spatial/location qualifiers
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
..... extension:biospecimenLaterality 0..1 code Laterality information for the site
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
.... 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(4.0.1) The total quantity of the specimen
.... method 0..1 CodeableConcept The approach used to collect the biospecimen (unknown if not provided)
.... 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
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:biospecimenAvailability 0..1 code Can this Sample be requested for further analysis?
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
..... extension:aliquotConcentration 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 0..* Identifier Unique ID for this aliquot
.... specimenQuantity 0..1 SimpleQuantity(4.0.1) What is the volume of the Aliquot?
... condition 0..* CodeableConcept How is the Sample stored, eg, Frozen or with additives

doco Documentation for this format

Constraints

Id Grade Path(s) Description Expression
collection-xor-parent warning Specimen If there is a parent sample, there should be no collection information. If there is collection information present, there should be no parent sample. parent.exists().not() or collection.exists().not()
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen C 0..* Specimen Sample for analysis
Constraints: collection-xor-parent
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... extension 0..* Extension Additional content defined by implementations
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* 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 Information about how the biospecimen was collected. Collection information may be unknown, but must be included when there is no parent sample
.... id 0..1 string Unique id for inter-element referencing
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:biospecimenSpatial 0..1 code Any spatial/location qualifiers
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
..... extension:biospecimenLaterality 0..1 code Laterality information for the site
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
.... 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(4.0.1) The total quantity of the specimen
.... method 0..1 CodeableConcept The approach used to collect the biospecimen (unknown if not provided)
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): Codes describing anatomical locations. May include laterality.
.... fastingStatus[x] Σ 0..1 Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.
..... fastingStatusCodeableConcept CodeableConcept
..... fastingStatusDuration Duration
... processing 0..* BackboneElement Processing and processing step details
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... description 0..1 string Textual description of procedure
.... procedure 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
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:biospecimenAvailability 0..1 code Can this Sample be requested for further analysis?
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
..... extension:aliquotConcentration 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 ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... identifier Σ 0..* 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: SpecimenContainerType (example): Type of specimen container.
.... capacity 0..1 SimpleQuantity(4.0.1) Container volume or size
.... specimenQuantity 0..1 SimpleQuantity(4.0.1) 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

doco Documentation for this format

Terminology Bindings

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

Constraints

Id Grade Path(s) Description Expression
collection-xor-parent warning Specimen If there is a parent sample, there should be no collection information. If there is collection information present, there should be no parent sample. parent.exists().not() or collection.exists().not()
dom-2 error Specimen If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Specimen If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Specimen If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Specimen If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Specimen A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen C 0..* Specimen Sample for analysis
Constraints: collection-xor-parent
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* Identifier Unique ID for this sample
... 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
... collection 0..1 BackboneElement Information about how the biospecimen was collected. Collection information may be unknown, but must be included when there is no parent sample
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:biospecimenSpatial 0..1 code Any spatial/location qualifiers
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
..... extension:biospecimenLaterality 0..1 code Laterality information for the site
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... 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)
.... quantity 0..1 SimpleQuantity(4.0.1) The total quantity of the specimen
.... method 0..1 CodeableConcept The approach used to collect the biospecimen (unknown if not provided)
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): Codes describing anatomical locations. May include laterality.
... 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.

doco Documentation for this format

Terminology Bindings

Path Status Usage ValueSet Version Source
Specimen.status Base required SpecimenStatus 📍4.0.1 FHIR Std.
Specimen.type Base example hl7VS-specimenType 📦2.0.0 THO v7.0
Specimen.collection.​method Base example FHIR Specimen Collection Method 📍4.0.1 FHIR Std.
Specimen.collection.​bodySite Base example SNOMED CT Body Structures 📍4.0.1 FHIR Std.
Specimen.condition Base extensible hl7VS-specimenCondition 📦2.0.0 THO v7.0

Constraints

Id Grade Path(s) Description Expression
collection-xor-parent warning Specimen If there is a parent sample, there should be no collection information. If there is collection information present, there should be no parent sample. parent.exists().not() or collection.exists().not()
dom-2 error Specimen If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Specimen If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Specimen If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Specimen If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Specimen A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

Differential View

This structure is derived from Specimen

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen C 0..* Specimen Sample for analysis
Constraints: collection-xor-parent
... identifier 0..* 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
... parent 0..* Reference(Specimen) The Sample from which this Sample was derived
... collection 0..1 BackboneElement Information about how the biospecimen was collected. Collection information may be unknown, but must be included when there is no parent sample
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:biospecimenSpatial 0..1 code Any spatial/location qualifiers
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
..... extension:biospecimenLaterality 0..1 code Laterality information for the site
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
.... 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(4.0.1) The total quantity of the specimen
.... method 0..1 CodeableConcept The approach used to collect the biospecimen (unknown if not provided)
.... 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
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:biospecimenAvailability 0..1 code Can this Sample be requested for further analysis?
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
..... extension:aliquotConcentration 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 0..* Identifier Unique ID for this aliquot
.... specimenQuantity 0..1 SimpleQuantity(4.0.1) What is the volume of the Aliquot?
... condition 0..* CodeableConcept How is the Sample stored, eg, Frozen or with additives

doco Documentation for this format

Constraints

Id Grade Path(s) Description Expression
collection-xor-parent warning Specimen If there is a parent sample, there should be no collection information. If there is collection information present, there should be no parent sample. parent.exists().not() or collection.exists().not()

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. Specimen C 0..* Specimen Sample for analysis
Constraints: collection-xor-parent
... id Σ 0..1 id Logical id of this artifact
... meta Σ 0..1 Meta Metadata about the resource
... implicitRules ?!Σ 0..1 uri A set of rules under which this content was created
... text 0..1 Narrative Text summary of the resource, for human interpretation
This profile does not constrain the narrative in regard to content, language, or traceability to data elements
... contained 0..* Resource Contained, inline Resources
... extension 0..* Extension Additional content defined by implementations
... modifierExtension ?! 0..* Extension Extensions that cannot be ignored
... identifier Σ 0..* 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 Information about how the biospecimen was collected. Collection information may be unknown, but must be included when there is no parent sample
.... id 0..1 string Unique id for inter-element referencing
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:biospecimenSpatial 0..1 code Any spatial/location qualifiers
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial
..... extension:biospecimenLaterality 0..1 code Laterality information for the site
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality
.... 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(4.0.1) The total quantity of the specimen
.... method 0..1 CodeableConcept The approach used to collect the biospecimen (unknown if not provided)
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): Codes describing anatomical locations. May include laterality.
.... fastingStatus[x] Σ 0..1 Whether or how long patient abstained from food and/or drink
Binding: hl7VS-relevantClincialInformation (extensible): Codes describing the fasting status of the patient.
..... fastingStatusCodeableConcept CodeableConcept
..... fastingStatusDuration Duration
... processing 0..* BackboneElement Processing and processing step details
.... id 0..1 string Unique id for inter-element referencing
.... extension 0..* Extension Additional content defined by implementations
.... modifierExtension ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... description 0..1 string Textual description of procedure
.... procedure 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
.... Slices for extension 0..* Extension Extension
Slice: Unordered, Open by value:url
..... extension:biospecimenAvailability 0..1 code Can this Sample be requested for further analysis?
URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/aliquot-availability
..... extension:aliquotConcentration 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 ?!Σ 0..* Extension Extensions that cannot be ignored even if unrecognized
.... identifier Σ 0..* 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: SpecimenContainerType (example): Type of specimen container.
.... capacity 0..1 SimpleQuantity(4.0.1) Container volume or size
.... specimenQuantity 0..1 SimpleQuantity(4.0.1) 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

doco Documentation for this format

Terminology Bindings

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

Constraints

Id Grade Path(s) Description Expression
collection-xor-parent warning Specimen If there is a parent sample, there should be no collection information. If there is collection information present, there should be no parent sample. parent.exists().not() or collection.exists().not()
dom-2 error Specimen If the resource is contained in another resource, it SHALL NOT contain nested Resources contained.contained.empty()
dom-3 error Specimen If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4 error Specimen If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5 error Specimen If a resource is contained in another resource, it SHALL NOT have a security label contained.meta.security.empty()
dom-6 best practice Specimen A resource should have narrative for robust management text.`div`.exists()
ele-1 error **ALL** elements All FHIR elements must have a @value or children hasValue() or (children().count() > id.count())
ext-1 error **ALL** extensions Must have either extensions or value[x], not both extension.exists() != value.exists()

 

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