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 (Version 2.0.0 - STU2 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. Over the past few years, laboratories have been forming regional pathology networks.

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.

Pathology Data Products

This implementation guide has been developed by the Pathology Standards and Implementation team within NHS England. The team has also developed a SNOMED CT® based catalogue of pathology laboratory test request and test result codes. This catalogue was previously known as the Unified Test List (UTL). The UTL was originally a relatively simple set of codes representing pathology laboratory test requests and results, with each code carrying a SNOMED CT concept identifier. Following extensive modelling and classification work, the UTL has evolved into 'true' SNOMED CT. The content is accessible via two 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

In addition to the PaLM reference sets, the following additional SNOMED CT reference set is also available to use:

  • 999002881000000100 | Pathology Bounded Code List (PBCL) observables simple reference set - containing laboratory test result codes

The PBCL was originally a subset of Read v2 codes for use in laboratory to GP practice messaging. Semantically equivalent SNOMED CT PBCL concepts were created for migration to SNOMED CT in primary care, and these are contained in the PBCL observables simple reference set.

The Read code based version of the PBCL is currently used in conjunction with the PMIP EDIFACT (NHS003) messaging specification. The PMIP EDIFACT (NHS003) specification defines the data structure of pathology test reports that flow between laboratories and GP practices. The current GP practice related pathology data flows are described in detail in the Background section of this implementation guide. Further information on the use of SNOMED CT for pathology reporting can be found on the Pathology Standards and Implementation website.

Together with this implementation guide, the PaLM and PBCL SNOMED CT reference sets form a group of related data products. These products will initially be used to replace PMIP EDIFACT (NHS003) and the PBCL. There is an urgent need to replace the use of PMIP EDIFACT (NHS003) due to the following fundamental limitations:

  • it is unable to carry SNOMED CT test result concepts - it can only support Read codes; the final release of Read CTV3 was in April 2018 consequently it has not been possible to create new PBCL Read codes since then
  • it is unable to support complex report structures using fully atomic, coded results - the data elements of complex reports are mainly represented in PMIP EDIFACT (NHS003) as text with limited clinical coding
  • due to the age of the underlying EDIFACT standard, its continued use is a significant barrier to new market entrant system suppliers

Scope

The current scope of this implementation guide reflects the priority of replacing PMIP EDIFACT (NHS003) and the 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 PaLM and PBCL SNOMED CT 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

Implementation Guide Structure

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.
    • 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.
  • Build:
  • 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 any ValueSets that are particularly relevant to 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: