Pathology FHIR specification

Fast Healthcare Interoperability Resources (FHIR) is a standards framework that is used for healthcare data exchange. In this context, it is used to define the structure of pathology laboratory test reports.

In the pathology laboratory to GP practice data flow, test reports are currently represented using the data structure defined in the PMIP EDIFACT (NHS003) specification. As described in the DAPB4101 Pathology and Laboratory Medicine Reporting Information Standard, PMIP EDIFACT (NHS003) will be replaced by a specification based on FHIR. Each pathology report will be represented by a FHIR UK Core R4 ‘bundle’ and will include:

• SNOMED CT Observable entity concepts to represent the laboratory test result code
• SNOMED CT Procedure concepts to represent test panels/batteries within the test report
• SNOMED CT Procedure concepts to represent the specific laboratory test initially requested

Download a diagram that illustrates the structure of an example HbA1c and serum lipid level laboratory test report

The Pathology Standards and Implementation team have created pathology-specific FHIR UK Core R4 profiles and an accompanying implementation guide:

The Pathology FHIR implementation guide provides the detailed guidance system suppliers will need to implement the pathology-related FHIR profiles. Regularly updated, this FHIR implementation guide is referenced in DAPB4101’s implementation guidance as the source of truth for implementors.

Additional information can be found in the Pathology Messaging - FHIR section of the NHS England API and integration catalogue.

NHS England's Message Exchange for Social Care and Health (MESH) service supports the ability to share data directly and securely between health and care organisations. MESH is the nationally recognised mechanism for message-based data sharing and is currently used to transport PMIP EDIFACT reports from laboratory systems to GP systems.

In addition to MESH, FHIR supports other methods of exchanging data, including the use of RESTful APIs. This approach may be considered for pathology reporting in the future, but until an alternative national messaging architecture is mandated, MESH will be used to transport FHIR UK Core R4 pathology reports.

The ISB 1557 EDIFACT Pathology Messaging Standard (Amd 39/2003 EDIFACT v1.003) underpins the Pathology Messaging - EDIFACT integration (PMIP EDIFACT).

The standard is fundamentally limited because:

• it is unable to carry SNOMED CT encoded test result concepts - it can only support Read v2 Pathology Bounded Code List (PBCL) codes
• it is unable to support complex report structures containing fully atomic, coded results – data elements are mainly represented as text
• the continued use of PMIP EDIFACT is a significant barrier to new market entrants who struggle to implement a messaging technology that is over 30 years old, and not aligned with modern standards such as FHIR

The risk associated with PMIP EDIFACT’s inability to carry SNOMED CT encoded data was realised as a significant issue in 2020, when the COVID-19 pandemic emerged. The SNOMED CT concepts authored to represent COVID-19 could not be carried by PMIP EDIFACT. This resulted in a huge problem as vast amounts of COVID testing data needed to flow from laboratories to general practice. The issue was mitigated solely by costly and temporary workaround solutions, unsustainable in the long term. NHS England must work to ensure that the same situation does not occur again.

There are also a growing number of new laboratory test request and result types that cannot flow into GP systems in a computable format due to the deprecation of Read v2, and PMIP EDIFACT’s inability to transport the SNOMED CT concepts authored to represent them.

This replacement is also a professional requirement supported by members of the Royal College of GPs and the Royal College of Pathologists.

ISB 1557 is scheduled for deprecation in April 2024.