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

Logical Model: Shared Data Model for Biospecimen Collection

Official URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelBiospecimenCollection Version: 0.2.0
Draft as of 2025-12-03 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).

Usages:

  • This Logical Model is not used by any profiles in this Implementation Guide

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
.. SharedDataModelBiospecimenCollection 0..* Base Shared Data Model for Biospecimen Collection
... sampleGenerated 1..1 VSReference(5.2.0) Sample that was generated from this collection event
... participant 1..1 VSReference(5.2.0) 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.
... 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

doco Documentation for this format

This structure is derived from Base

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. SharedDataModelBiospecimenCollection 0..* Base Shared Data Model for Biospecimen Collection
... sampleGenerated 1..1 VSReference(5.2.0) Sample that was generated from this collection event
... participant 1..1 VSReference(5.2.0) 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.
... 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

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. SharedDataModelBiospecimenCollection 0..* Base Shared Data Model for Biospecimen Collection
... sampleGenerated 1..1 VSReference(5.2.0) Sample that was generated from this collection event
... participant 1..1 VSReference(5.2.0) 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.
... 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

doco Documentation for this format

This structure is derived from Base

Summary

Mandatory: 0 element(2 nested mandatory elements)

Structures

This structure refers to these other structures:

Key Elements View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. SharedDataModelBiospecimenCollection 0..* Base Shared Data Model for Biospecimen Collection
... sampleGenerated 1..1 VSReference(5.2.0) Sample that was generated from this collection event
... participant 1..1 VSReference(5.2.0) 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.
... 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

doco Documentation for this format

Differential View

This structure is derived from Base

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. SharedDataModelBiospecimenCollection 0..* Base Shared Data Model for Biospecimen Collection
... sampleGenerated 1..1 VSReference(5.2.0) Sample that was generated from this collection event
... participant 1..1 VSReference(5.2.0) 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.
... 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

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraints    Filter: Filtersdoco
.. SharedDataModelBiospecimenCollection 0..* Base Shared Data Model for Biospecimen Collection
... sampleGenerated 1..1 VSReference(5.2.0) Sample that was generated from this collection event
... participant 1..1 VSReference(5.2.0) 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.
... 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

doco Documentation for this format

This structure is derived from Base

Summary

Mandatory: 0 element(2 nested mandatory elements)

Structures

This structure refers to these other structures:

 

Other representations of profile: CSV, Excel