Notice
- Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
- This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.
Extracted Specimen
Purpose
For testing, obtained from raw specimen To support storage, testing and interpretation.
Notes
Mapped to Specimen. It is expected extracted specimens will be additional specimens referencing the parent specimen via the Specimen.parent field.
Mapping
| Source Data item | Target FHIR Element | HL7v2.5.1 Mapping | Description |
|---|---|---|---|
| Extracted specimen - Type | Specimen.type Note: The ValueSet for this field is pending review to align with MDSv1.03 | SPM-4 | Tissue of origin. |
| Extracted specimen - State | Specimen.condition Note: The ValueSet for this field is pending review to align with MDSv1.03 | SPM-24 | How has the specimen been preserved/fixed. |
| Extracted specimen - Extracted date | Specimen.processing.timeDateTime where Specimen.processing.procedure = 62972009, alternatively, could use Specimen.collection.collectedDateTime for the new Specimen | OBR-7 attached to processing procedure in SAC-30 | Date at which a specimen was extracted from a previous specimen. |
| Extracted specimen - Id assigning authority ODS code (many) | Specimen.identifier.assigner | SPM-2.1.2 | Authority who assigned the specimen id. |
| Extracted specimen - Id (many) | Specimen.identifier.value | SPM-2 | Id of sample provided linked to the previously stated assigning authority. Occurs multiple times. |
| Extracted specimen - Location details | Not in scope for FHIR r4, could be attached to Tasks assigned to particular organizations, see also location details field under Raw Specimen/Biopsy | SAC-15 | Where a raw specimen is in storage and not provided with a request. |
| Extracted specimen - Additional specimen information | Observation resources referencing Specimen for coded information or Specimen.note | OBX segments attached to SPM | Raw specimen/biopsy - Additional specimen/biopsy information. |
| Extracted specimen - Sample well identifier | Specimen.container.identifier | SAC-3 | Id of the sample well. |