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 provides a detailed represention of how the high-level logical information model described above is realised in FHIR. The arrows represent the direction of the references between the resources.

Design Approach

The base FHIR R4 specification describes several methods of representing test reports and grouping observations. The design approach that has been adopted as part of this implementation guide is 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 (using distinct profiles) and are referenced from DiagnosticReport using DiagnosticReport.result.
• Observation.hasMember relationships are used to link test result Observations to the associated test group Observation.
• 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 (MCS) 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 following simplified data model illustrates the key aspects of this design approach for an example 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 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
• The code element of UKCore-Observation-Group-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 representing the test group
• 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 representing the requested test or test group
• The type element of UKCore-Specimen SHALL be populated using one of the following:
  • descendantOf 105590001 | Substance (in which case Specimen.collection.method and Specimen.collection.bodySite SHOULD also be populated), OR
  • descendantOf 49755003 | Morphologically abnormal structure, OR
  • descendantOf 123037004 | Body structure, OR
  • descendantOf 123038009 | Specimen, OR
  • descendantOf 260787004 | Physical object

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

Further information on the use of SNOMED CT for pathology reporting can be found on the Pathology Standards and 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 (HBsAg): 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 SHOULD be used
• for semi-quantitative and qualitative results, valueCodeable SHOULD be used, with a suitable SNOMED CT concept, for example: 260385009 Negative
• for narrative results, valueString SHOULD 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 the UKCore-Observation-Lab profile definition for further information relating to the representation of test results.