Implementing Laboratory Tests in openEHR

Owned by Ian McNicoll
Last updated: 05-Nov-2019 by Thomas Beale
14 min read

A. Laboratory ‘Panels’

Most laboratory results in haematology, biochemistry, immunology and virology are expressed as single analytes or as panels. Microbiology and histopathology (anatomic pathology) reports have a different structure and are modelled differently, and are described elsewhere.

Overview

With the release of the laboratory Test series of archetype to Team Review, it was felt useful to provide guidance on the use of these archetypes, as, based on implementation experience, a very different approach is now suggested for handling laboratory tests.

Glossary

Laboratory Report : The overall report as received from the laboratory, generally a COMPOSITION, which will contain one or more ’Laboratory Tests’.

Laboratory Test: The container OBSERVATION which contains details of the ordered laboratory investigation and overall conclusions. Examples: “Urea and Electrolytes”, “Full blood count”, “Glucose”, “Prostate Cancer Histopathology”

Laboratory Result (Analyte): An individual result with a value. e.g. Hb, White cell count, Urea, Sodium, Glucose. A Lab Test may include only a single analyte or multiple analytes, often as part of a formal ‘Laboratory panel’.

Each Laboratory Result will have a name e.g. “Hb” and a Value e.g. “12.2g/dl”. The Name is generally coded, preferably with an external reference terminology like SNOMED CT, NPU or LOINC but local laboratory codes or controlled vocabularies are commonly used.

Laboratory Panel: A grouping of laboratory analytes, that generally reflect a grouped Test request, often aligned to the output of an automatic group analysis device. The exact make-up of a ‘laboratory panel’ varies between labs and lab analysers. i.e. The analytes included in a “Full blood Count”, whilst broadly similar, are not consistent across analysers.

Notes:

Where an individual analyte is requested the Test Name and the Result Name may be identical.

Contexts of modelling use

Laboratory tests need to modelled in two quite different ways…

1. Message-driven contexts

Laboratory results are most commonly imported automatically via a structured message such as HL7v2, though other national messaging standards exist. The message structures can be quite variable and identification of the lab test and lab analytes make use of terminology. The exact structure of the incoming data is highly variable, and will depend on laboratory policy, variability of adherence to national standards, the exact lab analyser device used.

In essence the modeller is at the mercy of the laboratory message, and the target models have to be able to cope with inconsistent structures and coding.

2. UI-driven contexts

In some circumstances, the modeller is asked to construct a dataset which replicates one or more laboratory tests to underpin data-entry screens, or perhaps to pull data from a specific device. In these cases the optimal structure and optimal coding of test and analyte names will be known, and can be specified in the models.

In some systems, both contexts will be required and he challenge is to find an approach that allows consistent querying and retrieval.

Previous modelling approaches

In previous modelling efforts, a generic OBSERVATION lab_test archetype was often specialised to represent common individual ‘lab analytes’ or ‘lab panels’ such as ‘Lipid Profiles’, ‘Full Blood count’. Whilst this can work well for specific UI-driven contexts, it is much less helpful in messaging-driven contexts.

The variable nature of laboratory messaging and, in particular, the variable content of lab panels, makes it difficult for technical teams to map such messages to archetypes where the analyte pattern is strongly modelled.

Proposed new modelling approach

  1.  Use a Generic OBSERVATION ‘laboratory test’ archetype as the basis for most, if not all laboratory tests, including microbiology and histopathology tests. This handles the ordered test name and other overall test-related data and is heavily aligned with the HL7v2 OBER segment and FHIR Diagnostic report resource.
  2.  Analyte (individual results) are handled by slotting in a variety of CLUSTER archetypes, the most common pattern being the simple tabular panel represented by CLUSTER.laboratory_test_panel. This pattern will handle the majority of tabular lab tests e.g. haematology and biochemistry. Other tests such as immunology may require different patterns and some specialities such as microbiology and histopathology will require more specific patterns. even where only a single analyte is reported, we recommend that it be carried within a laboratory panel structure to allow for consistent querying.
  3.  For tabular results in CLUSTER Laboratory Test Panel the result is carried as ‘Result Value’ with the name of the analyte as the Result Value /name attribute. This will normally be coded with a reference terminology.
  4.  It is not planned to try to create specific panel archetype specialisations or templates at international level, as, in practice the exact content of each panel varies enormously depending on the analyser and local lab terminology use. We make create a couple of exemplars for demo purposes, or where very specific additional metadata is required e.g. Glucose tolerance testing.
  5.  If, at a national or local level, it appears possible to construct more definitive ‘hard-wired’ representations of lab panels, this should be done by analytes and possible units via templating. Some examples will be provided in the international CKM but this will largely have to be a local exercise since it is highly dependent on local terminology use and messaging.
  6.  Microbiology is particularly difficult as their is a lack of consistent reporting of micro results. Experience shows that it is generally better to work with a more generic archetype which can respond to incoming data at run-time but we will attempt to define aspects of micro reporting, such as antibiotic sensitivities, for which clear standard patterns are emerging.

Ian McNicoll to check the following.

This approach produces the 2 variant hierarchy of lab result data for biochemistry and haematology. The first is a pattern where a Lab test result Observation directly contains one or more analytes, each of which is a Cluster.

  • OBSERVATION – Lab test result - openEHR-EHR-OBSERVATION.laboratory_test_result.v1
    • data/events/data:
      •  ITEM_TREE
        • items:
          • ELEMENT – Test Name
          • CLUSTER – Specimen detail ← Archetype
          • etc
          • CLUSTER – Test Findings ← Archetype lab analyte - triglycerides
            • items
              •  ELEMENT
                • value
                  • QUANTITY
          • CLUSTER – Test Findings ← Archetype lab analyte - LDL
            • items
              •  ELEMENT
                • value
                  • QUANTITY
          • CLUSTER – Test Findings ← Archetype lab analyte - HDL
            • items
              •  ELEMENT
                • value
                  • QUANTITY

The second is a structure in which the Test Findings are a panel, e.g:

More generally, a free mixture of Panels and single Analytes could be used.


PROBLEM: querying paths are different if one pattern is not consistently used for the same kinds of analyte. E.g. if serum sodium and serum potassium are imported from a message feed and included under a panel by one implementation, but directly by another, and both implementations feed data to the same health record, there will be a problem querying, unless the CONTAINS operator is used.

Use Cases

In the following:

  • (1) - Different labs sending different configurations of the same exam
  • (2) - Different results for the same analyte

Analytes in same test result with relative (%) and absolute Quantity values (1,2)

(Ack: Former user (Deleted) from Core Consulting, Brasilia)

Leucogram (Panel)
(analyte)Leucocytes	      -		5.800/mm3
(analyte)Linfocytes	    19%		1.102/mm3
(analyte)Eosinophiles	 1%		   58/mm3

Results in absolute and relative values. The relative representation is not mandatory. In this example, leucocytes are only reported as absolute values, since they are the parameter for the relative calculation of the other analytes in white cell count.

This implies an analyte archetype structure like the following:

-- ADL2 syntax

CLUSTER[id9] matches {
    items matches {
		ELEMENT[id2.1] matches {	-- absolute value
    		value matches {
				DV_QUANTITY[id0.1] matches {
					normal_range matches {
						DV_INTERVAL<DV_QUANTITY>[id0.2] 
					}
					other_reference_ranges matches {
						REFERENCE_RANGE<DV_QUANTITY>[id0.3]
					}
				}
			}
        }
		ELEMENT[id2.2] matches {	-- relative value
    		value matches {
				DV_QUANTITY[id0.4] matches {
					units matches {"%"}
					normal_range matches {
						DV_INTERVAL<DV_QUANTITY>[id0.5] 
					}
					other_reference_ranges matches {
						REFERENCE_RANGE<DV_QUANTITY>[id0.6]
					}
				}
			}
        }
    }
}

Quantitative analytes in same test result with 2 units (1,2)

(Ack: Former user (Deleted) from Core Consulting, Brasilia)

Some labs report results for the same analyte in 2 different units for better interpretation, e.g. (nmol/L; pg/mL) (mg/dL; mmol/L), resulting in two distinct values for the same analyte. At the same time, labs may adopt different units for the same exam.

Analytes with both Quantity and Text/code value (1,2)

(Ack: Former user (Deleted) from Core Consulting, Brasilia)

Antibiogram (Panel)
(analyte) Amoxicillin	  > 2 mcg/mL 	Sensible
(analyte) Sulfadiazine	 > 64 mcg/mL	Resistant
(analyte) Cefalexine	> 0,5 mcg/mL	Sensible

This example illustrates scenarios in which some labs may use only one data type, whereas others may report the same result in two different ways.

This implies an analyte archetype structure like the following:

-- ADL2 syntax

CLUSTER[id9] matches {
    items matches {
		ELEMENT[id2.1] matches {	-- quantity
    		value matches {
				DV_QUANTITY[id0.1] matches {
					normal_range matches {
						DV_INTERVAL<DV_QUANTITY>[id0.2] 
					}
					other_reference_ranges matches {
						REFERENCE_RANGE<DV_QUANTITY>[id0.3]
					}
				}
			}
        }
		ELEMENT[id2.2] matches {	-- text value
    		value matches {
				DV_TEXT[id0.4]
			}
        }
    }
}

Microbiology result - what is the analyte? (2)

(Ack: Former user (Deleted) from Core Consulting, Brasilia)

Blood culture (panel)

Streptococcus pneumoniae	> 100.000 CFU/mL

This is specifically related to microbiology results, how to deal with analyte elements when the result of the exam is the analyte itself, being a DATA_VALUE for the Result data element? There is no specific analyte being searched (in most cases) in this scenario. How to query?
This is an example of two DATA_VALUEs for the same exam.

Analyte with quantitative value and qualitative reference range (1,2)

(Ack: Former user (Deleted) from Core Consulting, Brasilia)

Urianalysis (panel)	
						(val)	(reference)
(analyte)Glucose		+++		Absent

This implies a DV_ORDINAL  for the value but a code/text for the normal_range and reference_ranges. This could be simulated by using DV_ORDINAL for both, i.e. something like this:

-- ADL2 syntax

CLUSTER[id9] matches {
    items matches {
		ELEMENT[id2.1] matches {	-- quantity
    		value matches {
				DV_ORDINAL[id0.1] matches {
					normal_range matches {
						DV_INTERVAL<DV_ORDINAL>[id0.2] 
					}
					other_reference_ranges matches {
						REFERENCE_RANGE<DV_ORDINAL>[id0.3]
					}
				}
			}
        }
    }
}

Same result in different format, depending on lab (1)

(Ack: Former user (Deleted) from Core Consulting, Brasilia)

In the following, Lab1 is reporting bilirubin as an ordinal with a code or text reference range, while lab 2 is reporting using two codes.

Lab1
Urianalysis (panel)

						Result 		Reference range
(analyte)Bilirubin		+++			Absent


Lab2
Urianalysis (panel)
						Result		Reference range
(analyte)Bilirubin		Moderate	Absent

Result format may vary depending on the analysis result. In urine strips testing, lab interpretation may present results as texts, scales or quantities, in different units. For example, protein analysis may result in "negative", "traces", "++" or "30 mg/dL". All this DATA-VALUES must be allowed in the result element. Not all results are automatic. Some are manual testings

Issue: how to register reference ranges for DV_TEXT, DV_ORDINAL results? Reference ranges often expands the "Normal"/"High" ranges, such as interpretation of clinical risks: cardiovascular risks, diabetes risk. Others may be interpreted as evidence for bacterial infection or viral infection depending on the result value (eg, for C-RP exams). There are examples that includes value ranges for specific interpretations, as: Negative: < 1,6 UI/mL; Indeterminate: 1,60 - 2,0 UI/mL; Positive: >= 3,00 UI/mL.

Template examples

Template for use in message-driven contexts.

An example of a template left generic to receive a variety of individual analytes or laboratory panels via a laboratory message can be found at http://openehr.org/ckm/#showTemplate_1013.26.185

Template for use in UI-driven contexts

An example of a template constructed to represent a lipid profile for use to underpin data-entry or where the exact incoming lipid profile panel is known and consistent, is at http://openehr.org/ckm/#showTemplate_1013.26.69

Instance Example “Structured JSON”:

This example of openEHR data in ‘Structured json’ format, shows how laboratory test names, laboratory result names and values appear in openEHR data. The data format and paths should be identical regardless of whether a UI-driven or message-driven template approach is used.


{
"laboratory_test#1": [
  {
    "test_name": [
        {
          "|code": "51990-0",
          "|value": "Basic metabolic panel- Blood",
          "|terminology": "SNOMED-CT"
        }
    ],
    "test_status": [
      {
        "|code": "at0038",
        "|value": "Final",
        "|terminology": "local"
      }
    ],
    "test_status_timestamp": [
        "2015-04-22T00:11:02.518+02:00"
    ],
    "laboratory_test_panel": [
      {
      "laboratory_result#1": [
        {
          "result_value": [
            {
             "_name": [
                {
                 "|value": "Urea",
                 "|code": "14937-7",
                 "|terminology": "LOINC"
                }
            ],
            "|magnitude": 7.8,
            "|unit": "mmol/l",
            "_normal_range": [
              {
                "lower": [
                    {
                    "|unit": "mmol/l",
                    "|magnitude": 2.5
                    }
                ],
                "upper": [
                  {
                    "|unit": "mmol/l",
                    "|magnitude": 6.6
                  }
                ]
              }
            ]
            },
          ],
          "comment": [
            "may be technical artefact"
          ]
        },
      ],
      "laboratory_result#2": [
        {
        "result_value": [
          {
            "_name": [
            {
              "|value": "Creatinine",
              "|code": "14682-9",
              "|terminology": "LOINC"
            }
          ],
            "|magnitude": 123,
            "|unit": "mmol/l",
            "_normal_range": [
            {
              "lower": [
                {
                "|unit": "mmol/l",
                "|magnitude": 80
                }
              ],
              "upper": [
                {
                "|unit": "mmol/l",
                "|magnitude": 110
                }
              ]
            }
          ]
        }
      ]
    },
  ],
  "conclusion": [
  "Very rapidly deteriorating renal function"
  ],
}
],
"laboratory_test#2": [
  {
    "test_name": [
        {
          "|code": "15074-8",
          "|value": "Glucose",
          "|terminology": "LOINC"
        }
    ],
    "test_status": [
      {
        "|code": "at0038",
        "|value": "Final",
        "|terminology": "local"
      }
    ],
    "test_status_timestamp": [
        "2015-04-22T00:11:02.518+02:00"
    ],
    "laboratory_test_panel": [
      {
      "laboratory_result": [
        {
          "result_value": [
            {
             "_name": [
                {
                 "|value": "Glucose",
                 "|code": "15074-8",
                 "|terminology": "LOINC"
                }
            ],
            "|magnitude": 4.2,
            "|unit": "mmol/l",
            "_normal_range": [
              {
                "lower": [
                  {
                  "|unit": "mmol/l",
                  "|magnitude": 1.3
                  }
                ],
                "upper": [
                  {
                  "|unit": "mmol/l",
                  "|magnitude": 6.6
                  }
                ]
              }
            ]
            }
          ]
        }
      ],
      "comment": [
        "may be technical artefact"
      ]
      }
    ],
    "conclusion": [
        "Normal for age"
    ]
  }
]
}