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.
Task Updates
Purpose
This category has been developed to facilitate translation between HL7v2 and FHIR for Task Updates.
Notes
Part of the Genomics Order Management Service vision is to support detailed Task management for genomic ServiceRequests. Current operational models struggle to break through the complexity and opacity of genomics lab workflows to provide meaningful periodic feedback to requesters. The GOMS task management system is an attempt to provide a standard set of genomics tasks which represent order processing checkpoints. These checkpoints are useful for operational reporting and metrics, as well as for detailed at-a-glance status updates which are more efficient than direct communication with performing labs.
GOMS tasks cover the following themes (illustrated by the Task.code CodeSystem: Genomic-Task-Code)
- When a lab receives a genomics test request
- When a lab receives the physical specimen associated with the test request (and the resulting sample/request alignment)
- When a lab has completed pre-analytical lab processes (e.g. aliquot, DNA/RNA extraction)
- When a lab has completed analytical lab processes (e.g. DNA/RNA sequencing)
- When a lab has completed data analysis (e.g. Gene identification and quantification)
- When a lab has completed interpretation of the genomic results
- When a lab has issued a preliminary report (e.g. confirmation testing in progress)
- If a lab result is being discussed at a genomics MDT
- When a lab has issued a final report
- When the final lab report has been acknowledged by the service requestor and communicated to the patient.
In translation from FHIR to HL7v2 when retrieving tasks, it is proposed the Tasks are copied into subsequent ORC and OBR repeating segments within the OML_O21 mesage for the original order (ideally with ORC-1=CH to represent a child request). These can then be processed into a directory order and sub orders within the receiving LIMS.
Sending Task updates from the LIMS to the GOMS broker should then be via result messages, e.g. ORU_O21 (for results) or OUL_R24 (for interim status messages). e.g. for specimen receipt, OUL_R24 with OBR-25=I. HL7v2 result messages SHALL be transformed into relevant Task or output resources, e.g. DiagnosticReport, at the source organisation, e.g. via the use of a Trust Integration Engine.
Output results in HL7v2 MAY be structured using the GenomeX Data Exchange FHIR IG guidance
Element Structural Mapping
Task Key Elements
Mappings for Key elements in Task which may be filled
| FHIR Element | HL7v2.5.1 Segment | Notes |
|---|---|---|
| status | ORC-1/ORC-5 | Based on whether the status is intermediate or final, see status code mapping table below |
| statusReason | ORC-16 | Using FHIR CodeSystem Genomic-Task-StatusReason |
| businessStatus | ORC-25 | Using FHIR CodeSystem Genomic-Business-Status |
| code | OBR-4 | Using FHIR CodeSystem Genomic-Task-Code, different mesasge types could also be used for different codes, see table below as some TBC |
| focus | ORC-8 | |
| for | PID-2 | |
| executionPeriod | TQ1-7/TQ1-8 | For start and end times |
| authoredOn | ORC-15 | |
| lastModified | ORC-9 | |
| requester | ORC-12 | |
| owner | OBR-46 | In HL7v2 the recipient is assumed to be the owner, though supplemental service information fields could be used to record the ODS code of the Task owner |
| note | NTE-3 | |
| input | NTE-3 | Depending on the input type, may be recorded in other segments |
| output | NTE-3 | Depending on the output type, may be recorded in other segments |
Element Code Concept Mapping
Task Codes
Based on the Task.code used, ideally a different HL7v2 message should be used as some tasks are related to results or specific to a specimen. TBC
| Task.code | HL7v2.5.1 Message | Notes |
|---|---|---|
| process-genomic-test-request | OUL_R24 | |
| request-sample-alignment | OUL_R24 | |
| sample-preparation | OUL_R24 | |
| sample-processing | OUL_R24 | |
| genetic-genomic-data-processing | OUL_R24 | |
| interpretation | OUL_R24 | |
| produce-interim-report | ORU_O21 | |
| genomic-mdt | OUL_R24 | |
| produce-final-report | ORU_O21 | |
| distribute-report | ORU_O21 |
Task Statuses
Mapped to codes within ORC-1/ORC-5 in the above messages
| Task.status | HL7v2.5.1 Mapping | Notes |
|---|---|---|
| Draft | N/A | No equivalent in HL7v2, draft Tasks may not be able to be injested into LIMS via HL7v2 |
| Requested | ORC-1=CH | NW is reserved for the ServiceRequest |
| Received | Not used in Genomics Order Management | |
| Accepted | ORC-1=OK | |
| Rejected | ORC-1=UA | |
| Ready | Not used in Genomics Order Management | |
| Cancelled | ORC-5=CA | Automatically set by the central broker |
| In Progress | ORC-5=IP | |
| On Hold | ORC-5=HD | Usually accompanied by a statusReason |
| Failed | ORC-5=DC | MAY be accompanied by a new Task awaiting Revocation of the ServiceRequest |
| Completed | ORC-5=CM | |
| Entered in Error | ORC-1=DE |
ServiceRequest Statuses
ServiceRequests statuses may also need to be mapped into HL7v2 Order Control Codes, as these are central to FHIR Workflow. This element does not appear within the MDS but proposed mappings for codes are provided below.
| Task.status | HL7v2.5.1 Mapping | Notes |
|---|---|---|
| Draft | N/A | No equivalent in HL7v2, draft ServiceRequests may not be able to be injested into LIMS via HL7v2 |
| Active | ORC-1=NW | |
| On Hold | ORC-1=HD | |
| Revoked | ORC-1=CA | |
| Completed | OCR-5=CM | For parent order |
| Entered in Error | ORC-1=DE | For parent order |
| Unknown | Not used in Genomics Order Management |