NCPI FHIR Implementation Guide v2
0.1.0 - ci-build

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 Sample

Official URL: https://nih-ncpi.github.io/ncpi-fhir-ig-2/StructureDefinition/SharedDataModelSample Version: 0.1.0
Draft as of 2024-09-26 Computable Name: CdmSample

Shared Data Model for Sample

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.

Sample

Samples are ideally “biologically equivalent” biospecimen. This may be an abstraction from real-world samples, but provide a helpful tool for simplifying potentially complex data recorded in LIMS. For example, a protocol may include several edta tubes of whole blood: those would be tracked separately in a LIMS, but a secondary data research consumer doesn’t need to know those details in most cases.

Samples can be derived from other samples or from a collection event. It’s possible to describe detailed processing chains, for example tracking Whole Blood -> WBCs -> DNA, but this is not required. *Only the collected biospecimen and any biospecimen used in analysis NEED to be recorded.

There are cases where tube contamination may present challenges that a user of this data may not be able to track without further information, but this is out of scope for our use case.

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

NameFlagsCard.TypeDescription & Constraintsdoco
.. SharedDataModelSample 0..* Base Shared Data Model for Sample
Instances of this logical model are not marked to be the target of a Reference
... sampleId 1..1 string Unique ID for this sample
... participant 1..1 VSReference(5.1.0) The participant from whom the biospecimen was taken
... parentSample 0..* VSReference(5.1.0) The Sample from which this Sample was derived
... processing 0..* code Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample
... availabilityStatus 0..1 code Can this Sample be requested for further analysis?
... storageMethod 0..* code How is the Sample stored, eg, Frozen or with additives
... quantity 0..1 Quantity The total quantity of the specimen

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. SharedDataModelSample 0..* Base Shared Data Model for Sample
Instances of this logical model are not marked to be the target of a Reference
... sampleId 1..1 string Unique ID for this sample
... participant 1..1 VSReference(5.1.0) The participant from whom the biospecimen was taken
... parentSample 0..* VSReference(5.1.0) The Sample from which this Sample was derived
... processing 0..* code Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample
... availabilityStatus 0..1 code Can this Sample be requested for further analysis?
... storageMethod 0..* code How is the Sample stored, eg, Frozen or with additives
... quantity 0..1 Quantity The total quantity of the specimen

doco Documentation for this format
NameFlagsCard.TypeDescription & Constraintsdoco
.. SharedDataModelSample 0..* Base Shared Data Model for Sample
Instances of this logical model are not marked to be the target of a Reference
... sampleId 1..1 string Unique ID for this sample
... participant 1..1 VSReference(5.1.0) The participant from whom the biospecimen was taken
... parentSample 0..* VSReference(5.1.0) The Sample from which this Sample was derived
... processing 0..* code Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample
... availabilityStatus 0..1 code Can this Sample be requested for further analysis?
... storageMethod 0..* code How is the Sample stored, eg, Frozen or with additives
... quantity 0..1 Quantity The total quantity of the specimen

doco Documentation for this format

This structure is derived from Base

Summary

Mandatory: 0 element(3 nested mandatory elements)

Structures

This structure refers to these other structures:

Differential View

This structure is derived from Base

NameFlagsCard.TypeDescription & Constraintsdoco
.. SharedDataModelSample 0..* Base Shared Data Model for Sample
Instances of this logical model are not marked to be the target of a Reference
... sampleId 1..1 string Unique ID for this sample
... participant 1..1 VSReference(5.1.0) The participant from whom the biospecimen was taken
... parentSample 0..* VSReference(5.1.0) The Sample from which this Sample was derived
... processing 0..* code Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample
... availabilityStatus 0..1 code Can this Sample be requested for further analysis?
... storageMethod 0..* code How is the Sample stored, eg, Frozen or with additives
... quantity 0..1 Quantity The total quantity of the specimen

doco Documentation for this format

Key Elements View

NameFlagsCard.TypeDescription & Constraintsdoco
.. SharedDataModelSample 0..* Base Shared Data Model for Sample
Instances of this logical model are not marked to be the target of a Reference
... sampleId 1..1 string Unique ID for this sample
... participant 1..1 VSReference(5.1.0) The participant from whom the biospecimen was taken
... parentSample 0..* VSReference(5.1.0) The Sample from which this Sample was derived
... processing 0..* code Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample
... availabilityStatus 0..1 code Can this Sample be requested for further analysis?
... storageMethod 0..* code How is the Sample stored, eg, Frozen or with additives
... quantity 0..1 Quantity The total quantity of the specimen

doco Documentation for this format

Snapshot View

NameFlagsCard.TypeDescription & Constraintsdoco
.. SharedDataModelSample 0..* Base Shared Data Model for Sample
Instances of this logical model are not marked to be the target of a Reference
... sampleId 1..1 string Unique ID for this sample
... participant 1..1 VSReference(5.1.0) The participant from whom the biospecimen was taken
... parentSample 0..* VSReference(5.1.0) The Sample from which this Sample was derived
... processing 0..* code Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample
... availabilityStatus 0..1 code Can this Sample be requested for further analysis?
... storageMethod 0..* code How is the Sample stored, eg, Frozen or with additives
... quantity 0..1 Quantity The total quantity of the specimen

doco Documentation for this format

This structure is derived from Base

Summary

Mandatory: 0 element(3 nested mandatory elements)

Structures

This structure refers to these other structures:

 

Other representations of profile: CSV, Excel