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
Logical Model: Shared Data Model for Biospecimen Collection
| Official URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelBiospecimenCollection | Version: 0.1.0 | |||
| Draft as of 2024-11-25 | Computable Name: CdmBiospecimenCollection | |||
Shared Data Model for Biospecimen Collection
NCPI Sample
Introduction
These entities are intended to present to users the history of samples used in a research study. They may also indicate potential availability of samples for request by other researchers. This model is specifically intended to express sample origins (Collection), sample flow and processing (Sample), and even specific stored tubes/slides (Aliquot). Conceptually, these represent the procedure at which the Biospecimen was collected (Collection), “biologically equivalent” samples in the path of processing (Sample), and specific tubes which may have a role in some circumstances (Aliquot).
A high level requirement from our common use cases is to understand “what sample was collected” and “what sample went into the assay”. This is important in genomics given “whole blood” vs “saliva” DNA analysis.
Biospecimen Collection
The Collection entity describes the collection procedure that generated the biospecimen. This can be very lightweight, for example just describing the age at collection and pointing to the Sample that was collected, or it can have robust information about the procedure, location, and laterality. Collection details are not required, but it should be indicated if a Sample was the “collected sample” (if known).
Usage:
- This Logical Model 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.
This structure is derived from Base
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
  SharedDataModelBiospecimenCollection |
0..* | Base | Shared Data Model for Biospecimen Collection Instances of this logical model are not marked to be the target of a Reference | |
  sampleGenerated |
1..1 | VSReference(5.1.0) | Sample that was generated from this collection event | |
| participant |
1..1 | VSReference(5.1.0) | The participant from whom the biospecimen was taken | |
| ageAtCollection |
0..1 | Quantity | The age at which this biospecimen was collected. Could be expressed with a term, an age, or an age range. | |
 method |
0..1 | code | The approach used to collect the biospecimen | |
| site |
0..1 | code | The location of the specimen collection | |
| spatial |
0..1 | code | Any spatial/location qualifiers | |
 laterality |
0..1 | code | Any spatial/location qualifiers | |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| SharedDataModelBiospecimenCollection |
0..* | Base | Shared Data Model for Biospecimen Collection Instances of this logical model are not marked to be the target of a Reference | |
| sampleGenerated |
1..1 | VSReference(5.1.0) | Sample that was generated from this collection event | |
| participant |
1..1 | VSReference(5.1.0) | The participant from whom the biospecimen was taken | |
| ageAtCollection |
0..1 | Quantity | The age at which this biospecimen was collected. Could be expressed with a term, an age, or an age range. | |
| method |
0..1 | code | The approach used to collect the biospecimen | |
| site |
0..1 | code | The location of the specimen collection | |
| spatial |
0..1 | code | Any spatial/location qualifiers | |
| laterality |
0..1 | code | Any spatial/location qualifiers | |
| Documentation for this format | ||||
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| SharedDataModelBiospecimenCollection |
0..* | Base | Shared Data Model for Biospecimen Collection Instances of this logical model are not marked to be the target of a Reference | |
| sampleGenerated |
1..1 | VSReference(5.1.0) | Sample that was generated from this collection event | |
| participant |
1..1 | VSReference(5.1.0) | The participant from whom the biospecimen was taken | |
| ageAtCollection |
0..1 | Quantity | The age at which this biospecimen was collected. Could be expressed with a term, an age, or an age range. | |
| method |
0..1 | code | The approach used to collect the biospecimen | |
| site |
0..1 | code | The location of the specimen collection | |
| spatial |
0..1 | code | Any spatial/location qualifiers | |
| laterality |
0..1 | code | Any spatial/location qualifiers | |
| Documentation for this format | ||||
This structure is derived from Base
Differential View
This structure is derived from Base
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| SharedDataModelBiospecimenCollection |
0..* | Base | Shared Data Model for Biospecimen Collection Instances of this logical model are not marked to be the target of a Reference | |
| sampleGenerated |
1..1 | VSReference(5.1.0) | Sample that was generated from this collection event | |
| participant |
1..1 | VSReference(5.1.0) | The participant from whom the biospecimen was taken | |
| ageAtCollection |
0..1 | Quantity | The age at which this biospecimen was collected. Could be expressed with a term, an age, or an age range. | |
| method |
0..1 | code | The approach used to collect the biospecimen | |
| site |
0..1 | code | The location of the specimen collection | |
| spatial |
0..1 | code | Any spatial/location qualifiers | |
| laterality |
0..1 | code | Any spatial/location qualifiers | |
| Documentation for this format | ||||
Key Elements View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| SharedDataModelBiospecimenCollection |
0..* | Base | Shared Data Model for Biospecimen Collection Instances of this logical model are not marked to be the target of a Reference | |
| sampleGenerated |
1..1 | VSReference(5.1.0) | Sample that was generated from this collection event | |
| participant |
1..1 | VSReference(5.1.0) | The participant from whom the biospecimen was taken | |
| ageAtCollection |
0..1 | Quantity | The age at which this biospecimen was collected. Could be expressed with a term, an age, or an age range. | |
| method |
0..1 | code | The approach used to collect the biospecimen | |
| site |
0..1 | code | The location of the specimen collection | |
| spatial |
0..1 | code | Any spatial/location qualifiers | |
| laterality |
0..1 | code | Any spatial/location qualifiers | |
| Documentation for this format | ||||
Snapshot View
| Name | Flags | Card. | Type | Description & Constraints |
|---|---|---|---|---|
| SharedDataModelBiospecimenCollection |
0..* | Base | Shared Data Model for Biospecimen Collection Instances of this logical model are not marked to be the target of a Reference | |
| sampleGenerated |
1..1 | VSReference(5.1.0) | Sample that was generated from this collection event | |
| participant |
1..1 | VSReference(5.1.0) | The participant from whom the biospecimen was taken | |
| ageAtCollection |
0..1 | Quantity | The age at which this biospecimen was collected. Could be expressed with a term, an age, or an age range. | |
| method |
0..1 | code | The approach used to collect the biospecimen | |
| site |
0..1 | code | The location of the specimen collection | |
| spatial |
0..1 | code | Any spatial/location qualifiers | |
| laterality |
0..1 | code | Any spatial/location qualifiers | |
| Documentation for this format | ||||
This structure is derived from Base