Pathology FHIR Implementation Guide

Introduction

This implementation guide and the HL7® FHIR® R4 assets that it references define a specification to enable the exchange of pathology laboratory data.

The implementation guide has been created by NHS England and forms part of the NHS England Programme Implementation Guides project on Simplifier®.

For the implementation guide version history, see Release Notes.

Note: The FHIR profiles that this implementation guide references are derived from the UK Core Implementation Guide (STU3 Sequence). Consequently this implementation guide (i.e. the Pathology FHIR Implementation Guide) must be read in conjunction with the UK Core Implementation Guide. A description of the published and development versions of the UK Core is provided in UK Core Publication (Version) History.

Pathology Overview

Pathology tests and investigations are critical to many aspects of patient care, supporting the diagnosis, treatment, monitoring and prevention of disease. Pathology comprises a broad range of specialities, each of which includes many individual tests. The key specialities can be grouped as follows:

  • blood sciences – this includes clinical biochemistry (also known as chemical pathology), haematology, immunology and transfusion medicine
  • microbiology – this includes bacteriology, virology and serology
  • cellular pathology – this includes cytology and histopathology
  • genetics – this includes clinical cytogenetics and molecular genetics

Pathology tests are requested by staff members in a variety of care provider organisations in primary care, secondary care and community settings. Within the NHS in England most pathology tests are performed by laboratories based in hospitals. Some pathology laboratories provide specialist and reference pathology testing services, often at a regional level.

An increasing number of pathology tests are performed outside of laboratories. These include tests that may be performed at a point of care (usually by a Health Care Professional in a care setting such as a GP practice or in a hospital ward) or by a patient or their carer at home.

The Background section of this implementation guide provides additional contextual information relating to pathology test requesting and reporting.

SNOMED CT for Pathology Reporting

NHS England has created a SNOMED CT® based catalogue of pathology laboratory test request and test result codes. Originally known as the Unified Test List (UTL), this catalogue began as a simple set of SNOMED CT codes. It has since evolved into a fully modelled set of test request and test result codes, available through the following SNOMED CT reference sets:

  • 1853561000000109 | PaLM (Pathology and Laboratory Medicine) procedure simple reference set - containing laboratory test request codes
  • 1853551000000106 | PaLM (Pathology and Laboratory Medicine) observable entity simple reference set - containing laboratory test result codes
  • 999002881000000100 | Pathology Bounded Code List (PBCL) observables simple reference set - containing laboratory test result codes

The Pathology Bounded Code List (PBCL) was originally defined as a subset of Read v2 codes. The SNOMED PBCL reference set listed above provides a semantically equivalent set of SNOMED codes to support the replacement of the Read PBCL.

Further information on the use of SNOMED CT for pathology reporting can be found on the Pathology Standards Implementation website.

DAPB4101: Pathology and Laboratory Medicine Reporting Information Standard

The Read PBCL is currently used in conjunction with the PMIP EDIFACT (NHS003) messaging specification. Together, they define the clinical coding and data structure used for pathology test reports exchanged between laboratory middleware systems and GP EPR systems. Details of this existing data flow are provided in the Background section of this implementation guide.

The FHIR profiles described in this implementation guide, together with the SNOMED PBCL and PaLM reference sets, will be used to replace PMIP EDIFACT (NHS003) and Read PBCL. The requirement to do this is mandated by the DAPB4101: Pathology and Laboratory Medicine Reporting Information Standard.

Scope

The current scope of this implementation guide reflects the priority of replacing PMIP EDIFACT (NHS003) and Read PBCL. In summary:

  • the initial focus is on the ability to support pathology test reporting for tests that are requested by GP practices (please note that it is possible to return details relating to the originally requested test as part of a test report)
  • the clinical payload that is currently supported by the implementation guide is aligned with the SNOMED PBCL and SNOMED PaLM reference sets, and covers the following pathology specialities:
    • blood sciences - clinical biochemistry (also known as chemical pathology), haematology, immunology and transfusion medicine
    • microbiology - bacteriology, virology and serology

How to Read This Guide

This guide is divided into the following sections and pages which are accessible from the top-level menu bar:

  • Home: Provides an introduction to pathology, describes various SNOMED CT pathology related data products and outlines the scope and structure of this implementation guide.
  • Design:
    • Background: Includes a high-level business process flow for pathology test requesting and reporting, links to various supporting artefacts (user stories, personas and journey maps) and describes the systems and data flows that are currently used to support GP practice requested pathology tests.
    • Design Overview: Includes a high-level business information model and a detailed FHIR data model, a summary of the design approach that has been adopted and a description of how SNOMED CT is used to populate key aspects of the pathology related FHIR profiles.
    • Data Mapping: Provides a set of data mappings between the FHIR profiles that are referenced by this implementation guide and the PMIP EDIFACT (NHS003) messaging specification.
    • How to Construct Bundles: Describes how to use the FHIR profiles that are referenced by this implementation guide to create FHIR Bundles for pathology test requests and reports.
    • Transport (TBC): This page will detail the data exchange approach that will be used as part of this implementation guide.
    • Error Handling (TBC): This page will describe any error handling that will be used as part of this implementation guide.
    • Acknowledgement Framework (TBC): This page will describe the acknowledge framework that will be used as part of this implementation guide.
  • FHIR Assets:
    • Profiles: Describes the profiles that are referenced by this implementation guide.
    • Extensions: Describes any extensions that are particularly relevant to pathology.
    • CodeSystems: Describes any CodeSystems that are particularly relevant to pathology.
    • ValueSets: Describes the ValueSets that have been created specifically for use in pathology.
    • CapabilityStatements: Describes the CapabilityStatement that has been created specifically for use in pathology.
    • MessageDefinitions: Describes the MessageDefinitions that have been created specifically for use in pathology.
  • Examples:
    • Examples Index: Lists the FHIR examples that are included in this implementation guide, categorised by resource type and pathology speciality.
  • Help and Support:
    • Contact Us: Provides details for contacting the authors of this implementation guide.
    • Release Notes: Summarises the changes that have been made to this implementation guide.
    • Glossary: Provides a definition of key abbreviations, acronyms and terms that are used in this implementation guide.
    • Sitemap: Lists all of the key sections and pages that are included in this implementation guide.

Refer to the following related implementation guidance: