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
Resource Profile: NCPI Sample
| Official URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/ncpi-sample | Version: 0.1.0 | |||
| Draft as of 2025-03-24 | 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.
Recommended Practices
- 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 |
Usage:
- Examples for this Resource Profile: Specimen/GSS123456-01-010 and Specimen/SA-000
Formal Views of Profile Content
Description of Profiles, Differentials, Snapshots and how the different presentations work.
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  Specimen |
C | 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 collection-no-parent: If there is no parent sample, collection information must be present. If there is collection information present, there should be no parent sample. parent-no-collection: If there is no collection information, a parent sample must be present. If there is a parent sample present, there should be no collection information. |
  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 |
 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 |
Σ | 1..1 | Identifier | Unique ID for this sample ele-1: All FHIR elements must have a @value or children |
| status |
?!Σ | 0..1 | code | Can this Sample be requested for further analysis? Binding: SpecimenStatus (required): Codes providing the status/availability of a specimen. ele-1: All FHIR elements must have a @value or children |
| type |
Σ | 1..1 | CodeableConcept | The type of material of which this Sample is comprised Binding: hl7VS-specimenType (example): The type of the specimen. ele-1: All FHIR elements must have a @value or children |
 subject |
Σ | 1..1 | Reference(Patient | Group | Device | Substance | Location) | The participant from whom the biospecimen was taken ele-1: All FHIR elements must have a @value or children |
| parent |
0..* | Reference(Specimen) | The Sample from which this Sample was derived ele-1: All FHIR elements must have a @value or children | |
 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 ele-1: All FHIR elements must have a @value or children unless an empty Parameters resource | |
  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:biospecimen-spatial |
0..1 | code | Any spatial/location qualifiers URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-spatial ele-1: All FHIR elements must have a @value or children unless an empty Parameters resource ext-1: Must have either extensions or value[x], not both | |
 extension:biospecimen-laterality |
0..1 | code | Laterality information for the site URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/biospecimen-laterality ele-1: All FHIR elements must have a @value or children unless an empty Parameters resource 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 |
| 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) ele-1: All FHIR elements must have a @value or children |
| quantity |
0..1 | SimpleQuantity | The total quantity of the specimen ele-1: All FHIR elements must have a @value or children | |
| method |
1..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. ele-1: All FHIR elements must have a @value or children | |
 bodySite |
0..1 | CodeableConcept | The location of the specimen collection Binding: SNOMEDCTBodyStructures (example): SNOMED CT Body site concepts ele-1: All FHIR elements must have a @value or children | |
| 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. ele-1: All FHIR elements must have a @value or children |
| Documentation for this format | ||||
Terminology Bindings
| Path | Conformance | ValueSet | URI |
| Specimen.status | required | SpecimenStatushttp://hl7.org/fhir/ValueSet/specimen-status|4.3.0from the FHIR Standard | |
| Specimen.type | example | Hl7VSSpecimenTypehttp://terminology.hl7.org/ValueSet/v2-0487 | |
| Specimen.collection.method | example | FHIRSpecimenCollectionMethodhttp://hl7.org/fhir/ValueSet/specimen-collection-methodfrom the FHIR Standard | |
| Specimen.collection.bodySite | example | SNOMEDCTBodyStructureshttp://hl7.org/fhir/ValueSet/body-sitefrom the FHIR Standard | |
| Specimen.condition | extensible | Hl7VSSpecimenConditionhttp://terminology.hl7.org/ValueSet/v2-0493 |
Constraints
| Id | Grade | Path(s) | Details | Requirements |
| collection-no-parent | error | Specimen | If there is no parent sample, collection information must be present. If there is collection information present, there should be no parent sample. : parent.empty() implies collection.exists() and collection.exists() implies parent.empty() | |
| 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() | |
| parent-no-collection | error | Specimen | If there is no collection information, a parent sample must be present. If there is a parent sample present, there should be no collection information. : collection.empty() implies parent.exists() and parent.exists() implies collection.empty() |
Other representations of profile: CSV, Excel, Schematron