Design Overview

Pathology Business Information Model and FHIR Profile Mapping

The following diagram is a high-level logical representation of the key business entities relating to pathology test requesting and reporting:

To aid clarity, individual and organisation type entities (e.g. Performer / Performing Organisation) have been combined in the diagram but may be referenced independently. Each business entity is summarised below, together with links to the corresponding FHIR R4 resource (as defined in the base FHIR R4 Specification) and FHIR UK Core R4 profile (as described in the Profiles section of this implementation guide).

Pathology FHIR Data Model

The following diagram shows the key relationships between each of the pathology related FHIR resources (and associated profiles). It illustrates how the high-level information model described above is represented using FHIR. The arrows show the direction of the references between the FHIR resources.

Key aspects of the data model are summarised below:

• DiagnosticReport contains the overall findings and clinical interpretation relating to one or more pathology tests.
• Test results and test groups are defined as Observations and are referenced from DiagnosticReport using DiagnosticReport.result.
• Observation.hasMember relationships are used to link test result Observations to an associated test group Observation. This is aligned with the Observation.hasMember grouping method described in the base FHIR R4 Specification.
• To indicate that an Observation represents a test group, Extension UKCore-ObservationOrganizer is used. This extension mirrors the organizer data element introduced in FHIR R6. Refer to the description of Observation.organizer in the base FHIR R6 Specification (Ballot - 3rd Draft) for further details.
• Multiple levels of test group Observations and test result Observations may be nested to support complex report structures, such as those used in Microscopy, Culture and Sensitivity (MC&S) reports.
• ServiceRequest is used to carry summary details relating to the test request that the test report was based on.
• If multiple tests or test groups are requested as part of the same “event” (generally by the same practitioner at the same time for the same subject), an instance of ServiceRequest is required for each requested test or test group. ServiceRequest.requisition acts as a common identifier to link the requests.
• The Specimen.request data element is used to reference the ServiceRequest that a specimen relates to. This should be used when a test was requested before the specimen was collected.
• It is also possible to link a ServiceRequest to a specimen using the ServiceRequest.specimen data element. This should be used when a test is requested and the specimen has already been collected.

The diagram below shows a simplified data model for an example pathology test report:

SNOMED CT Usage

SNOMED CT concepts are used to populate the following key data elements in the FHIR profiles described in this implementation guide:

• The code element of UKCore-DiagnosticReport-Lab SHALL be populated using the following fixed SNOMED CT record artifact concept and description:
  • 721981007 | Diagnostic studies report
• The code element of UKCore-Observation-Lab (Test Result) SHALL be populated using one of the following:
  • memberOf 1853551000000106 | PaLM (Pathology and Laboratory Medicine) observable entity simple reference set, OR
  • memberOf 999002881000000100 | PBCL (Pathology Bounded Code List) observables simple reference set, OR
  • if an Observable Entity concept from either of the above reference sets cannot be identified (e.g. if a local reportable has yet to be mapped to SNOMED, or if the reportable is not yet represented in SNOMED), then it is acceptable to use a local code
• The code element of UKCore-Observation-Lab (Test Group) SHALL be populated using one of the following:
  • memberOf 1853561000000109 | PaLM (Pathology and Laboratory Medicine) procedure simple reference set, OR
  • if a Procedure concept from the above reference set cannot be identified, use a SNOMED CT procedure code taken from descendantOf 386053000 | Evaluation procedure (procedure), OR
  • if the two methods described above fail to identify a suitable code, then it is acceptable to use a local code
• The code element of UKCore-ServiceRequest-Lab SHALL be populated using one of the following:
  • memberOf 1853561000000109 | PaLM (Pathology and Laboratory Medicine) procedure simple reference set, OR
  • if a Procedure concept from the above reference set cannot be identified, use a SNOMED CT procedure code taken from descendantOf 386053000 | Evaluation procedure (procedure), OR
  • if the two methods described above fail to identify a suitable code, then it is acceptable to use a local code

The use of these aspects of SNOMED CT is illustrated in the following simplified data model for an example pathology test report:

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

Representation of Different Types of Test Results

Laboratory test results are reported using a variety of forms. These are described below with supporting examples. Each example includes a link to a corresponding FHIR Observation example (all of the examples are also listed in the Examples Index).

• Quantitative Result: the result is expressed as a number, usually with an associated unit of measure. Comparators may be used to indicate that the actual value is greater than or less than the stated value. A range of values may be reported instead of a single value. Examples include:
  • Albumin: 47 g/L
  • eGFR: >90 mL/min/1.73m2
• Semi-quantitative Result: the result is expressed using a descriptor to indicate the relative degree of positivity or negativity based on a scale. The scale is not always formally defined. Semi-quantitative results are widely used in microbiology, particularly for reporting microscopy and culture test results to indicate the amount or level of growth of organisms. Examples include:
  • Epithelial Cells: +
  • Organism Susceptibility to Nitrofurantoin: RESISTANT
• Qualitative Result: the result is expressed using a descriptor to indicate positivity or negativity. The descriptors are usually defined as pairs, for example: positive/negative, detected/not detected, isolated/not isolated. In this respect, qualitative results can be seen as a subset of semi-quantitative results in that they contain only two scale points to indicate positivity or negativity. Examples include:
  • Hepatitis B Surface Antigen: NEGATIVE
  • MRSA Screening Test: NOT DETECTED
• Quantitative Result Combined with an Interpretation: in some cases, a result may contain a combination of quantitative and non-quantitative elements. The non-quantitative element is sometimes expressed separately as an interpretation to provide a categorical assessment of the quantitative value. Examples include:
  • Lymphocyte Count: 0.70 10*9/L LOW
  • Rubella IgG Antibody: >10 IU/ml DETECTED
• Narrative Result: the result is presented as text, for example:
  • Aerobic Blood Culture: No growth detected after 5 days incubation

The Observation.value[x] data element is used to represent the test result value. The [x] part of the element name is replaced with an appropriate data type, based on the type of result:

• for quantitative results, valueQuantity, valueRange or valueRatio SHALL be used
• for semi-quantitative and qualitative results, valueString SHALL be used
• for narrative results, valueString SHALL be used.

The Observation.interpretation data element is used to provide a coded, categorical assessment of a test result value. The code is taken from the ObservationInterpretationCodes FHIR value set. The associated test result value is usually quantitative and represented using valueQuantity, valueRange or valueRatio as described above.

Refer to UKCore-Observation-Lab (Test Result) for further information relating to the representation of test results.