NHS North West Genomics
2.2.0 - ci-build
NHS North West Genomics
2.2.0 - ci-build
NHS North West Genomics - Local Development build (v2.2.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions
NHS England Genomic Order Management Service (GOMS) FHIR API - future integration.
Task-based event and coordination model GOMS usesTask-based coordination followsTask polling methodGOMS itself isn't a specific clinical test - it's a national "order comms" system that lets a clinician (or another Genomic Medicine Service Alliance) place a genomics test order without needing to know in advance which laboratory will actually perform it, and receive the report back the same way.
flowchart LR
A[Clinician identifies<br/>need for genomics test] --> B[Order placed<br/>via GOMS]
B --> C[Order routed to<br/>performing laboratory]
C --> D[Testing<br/>performed]
D --> E[Report routed back<br/>via GOMS]
E --> F[Clinical decision]
| IHE Actor | Role |
|---|---|
| Order Placer | Other NHS Trusts / GMSAs - place Laboratory Orders that GOMS exposes on their behalf, commonly known in the NHS as Order Comms |
| Resource Access Provider | NHS England Genomic Order Management Service (GOMS) - exposes Laboratory Orders and results via a FHIR RESTful API |
| Intermediary | Regional Integration Engine (RIE) - retrieves/posts FHIR Transaction Bundles to and from GOMS, converting to/from HL7 v2 for internal LIMS |
| Order Filler | iGene (NW Genomics master LIMS) - receives orders converted from GOMS, same as any other LAB-1 order |
| Requestor (ILW) | NW Genomics (iGene) - sub-contracts orders out to other GMSAs via GOMS |
| Subcontractor (ILW, via GOMS) | External GMSA / LIMS - fulfils orders NW Genomics sub-contracts out via GOMS |
| Transaction | Description | Direction |
|---|---|---|
FHIR RESTful GET /Task (polling) |
RIE polls GOMS for new/updated Task resources, since Task events are not yet distributed as push notifications |
RIE → GOMS |
| PCC-44 (Resource Exchange) / FHIR RESTful read | RIE retrieves the FHIR Transaction Bundle representing a Laboratory Order (plus other GOMS interactions) | GOMS → RIE |
FHIR Transaction Bundle → HL7 v2 OML_O21/ORM_O01 (LAB-1 equivalent) |
RIE converts the retrieved Bundle into an HL7 v2 order for delivery to an internal LIMS | RIE → iGene |
HL7 v2 OML_O21/ORM_O01 → FHIR Message O21 → FHIR Transaction (future) |
Reverse of the above: NW Genomics sub-contracts an order out; RIE converts it to a FHIR Message and then a FHIR Transaction Bundle, and posts it to GOMS | iGene → RIE → GOMS |
There is currently no integration with GOMS. Laboratory Orders for the North West arrive via the mechanisms already described in Regional Integration Engine (RIE) - Current Process (direct HL7 v2 from NHS Trusts, or manual/paper order entry) - GOMS is a future additional source of orders, and a future additional route for delivering sub-contracted orders out to other Genomic Laboratory Hubs.
GOMS exposes Laboratory Orders and related resources (e.g. Patient, ServiceRequest) via a FHIR RESTful API. As described in notebook 09 - LIMS Integration with the Genomic Order Management Service, the process starts from a FHIR Transaction Bundle:
Events and workflow are coordinated via FHIR Task resources rather than messaging - GOMS's incorporation of the national service into FHIR Workflow. In Enterprise Integration Patterns terms, this is a Conversation pattern. At present, Task events are not distributed as push notifications, so they must instead be retrieved via polling (GET /Task) - the same method already used to retrieve StarLIMS work orders from the FHIR Repository (see StarLIMS / iGene Integration), as demonstrated in notebook 02 - Work Orders: A Worked Example.
Task resources (GET /Task).Task, the RIE retrieves the linked resources from GOMS using PCC-44 (Resource Exchange) interactions (and other interactions defined in the GOMS API), assembling them into a FHIR Transaction Bundle.OML_O21/ORM_O01 order.Note: Orders retrieved from GOMS currently focus on the proband (the child, in a family/trio scenario) - orders for other family members (parents / consultands) are excluded. This is because NW Genomics' LIMS does not currently support representing consultand orders. Such orders may instead relate to a different pathway - general genetic services referred by an NHS Trust to NW Services, rather than the diagnostic services this IG otherwise covers - but this has not yet been analysed, so this may not be correct.
sequenceDiagram
participant OP as Other NHS Trust / GMSA<br/>Order Placer
participant GOMS as GOMS<br/>Resource Access Provider
participant RIE as Regional Integration Engine (RIE)<br/>Intermediary
participant iGene as iGene<br/>Order Filler
OP ->> GOMS: Places Laboratory Order<br/>(FHIR RESTful)
loop Polling - no Task events distributed yet
RIE ->> GOMS: GET /Task
GOMS -->> RIE: New/updated Task resources
end
RIE ->> GOMS: PCC-44 - retrieve order resources<br/>(FHIR Transaction Bundle)
GOMS -->> RIE: FHIR Transaction Bundle
RIE ->> RIE: Convert Bundle to HL7 v2
RIE ->> iGene: OML_O21 / ORM_O01<br/>(as LAB-1)
GOMS can also be used to deliver orders that NW Genomics sub-contracts out to another Genomic Laboratory Hub - roughly the reverse of the process above:
OML_O21/ORM_O01 (the same as any other ILW sub-order).sequenceDiagram
participant iGene as iGene<br/>Requestor (ILW)
participant RIE as Regional Integration Engine (RIE)<br/>Intermediary
participant GOMS as GOMS<br/>Resource Access Provider
participant Ext as External GMSA / LIMS<br/>Subcontractor (ILW)
iGene ->> RIE: OML_O21 / ORM_O01<br/>(as LAB-35 sub-order)
RIE ->> RIE: Convert HL7 v2 to FHIR Message O21
RIE ->> RIE: Convert FHIR Message to FHIR Transaction
RIE ->> GOMS: POST FHIR Transaction Bundle
Ext ->> GOMS: Retrieves order (FHIR RESTful)
This fits inside the IHE Inter Laboratory Workflow, with NW Genomics acting as Requestor and the external GMSA acting as Subcontractor - the same LAB-35/LAB-36 relationship as Sub-orders LAB-35 and LAB-36, delivered via GOMS's FHIR RESTful API instead of a direct message exchange.
GOMS itself is an NHS England service using profiles from the FHIR Genomics Implementation Guide and UK Core, not this IG's own profiles - see the Examples below for the resource shapes it exposes.
Example order Bundles sourced from the FHIR Genomics Implementation Guide on Simplifier, via nw-gmsa/Testing:
Note: the three
NonWGSTestOrderFormexamples above (base, CancerSolidTumor, FetalScenario, Reanalysis) were previously adapted with North West-specific organisation/sender details; the remaining examples are otherwise unmodified copies of the Simplifier source, with only anid(where missing) and theBundleMessageprofile added for consistency with this IG's other message Bundle examples.
Includes:
See Developer Guides for the full notebook series.