2026-01-28 - Laboratory Terminology Standards WG Meeting

1

Microbiology structured reporting design

Summary

HL7 Europe is developing a white paper with recommendations for terminology patterns in structured microbiology reporting to feed into a FHIR IG. The group discussed representations for organism identification and susceptibility testing.

Rob's absence was noted, and it was decided to postpone the discussion on organism toxin for identification until his next session.

HL7 Europe White Paper on Microbiology Terminology

 Karim explained that the group is working to provide guidance rather than mandates, acknowledging the need for flexibility due to varying structured reporting requirements. They discussed using generic codes for organism identification and presence/identity properties, considering both nominal values and ordinal values. The group also touched on the potential for post-coordination of nucleic acid detection and the possibility of including number concentration information, though this needs further exploration.

PCR Testing Specificity Discussion

The group discussed the challenges and limitations of conducting generic PCR tests versus organism-specific tests, with Jim and Scott explaining that PCR requires specific probes for accurate organism identification. They agreed that Option 2 (specific organism identification) was preferable to Option 3 (generic reporting code) for PCR testing due to the need for specific probes. The discussion also covered the differences between colony counts and nucleic acid quantitation, with Stan and James noting that these are fundamentally different measurements and should not be treated as equivalent. Gunnar mentioned a parallel discussion with Swedish microbiologists about culture information modeling, and Karim agreed to share the slides with the Swedish group for their input.

Susceptibility Testing in SNOMED

Stan and Karim discussed options for representing susceptibility testing in SNOMED. Stan expressed a slight preference for option 2, which allows for post-coordination of susceptibility results without specifying the exact testing method. They also discussed the distinction between MIC and susceptibility as separate properties in the NPU. Gunnar explained that in their pilot project, they have not yet created examples of susceptibility mapping to SNOMED.

Stan expressed concerns about the modeling of mass and substance concentrations in MIC, suggesting a need for review to ensure accuracy. Gunnar emphasized the importance of the NPU model and proposed mapping between NPU and LOINC concepts. Karim highlighted the need for clarification on the properties and conversions in the LOINC content, suggesting a potential discussion with the HL7 group.

• Stan: Review and verify that the SNOMED models for mean inhibitory concentration susceptibility tests are modeled correctly, particularly regarding whether they should use concentration properties or ordinal properties

• Gunnar: Share slides and discussion from Swedish microbiologists meeting about specific and non-specific cultures with the group

• Gunnar: Add the NPU model for susceptibility testing to compare with the SNOMED/LOINC model - Karim will follow up with Gunnar

• Karim: Bring up the susceptibility property modeling questions when the HL7 Lab Semantic Working Group discusses susceptibility specifics

• Karim: Relate the number concentration question back to the HL7 Lab Semantic Working Group who are currently working on identification steps

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AOB

1

SARS-Cov2 observable entity concepts for reporting viral RNA presence in the SNOMED CT International Edition

FA

These concepts are modelled with both inheres_in and direct_site

Farzaneh to take these back and discuss internally for a steer on the use of inheres_in for these concepts

On hold

SI propose to remove inheres_in but await formal decision from this group

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6

1

Time aspect specification in description AND modelling

All

Concept is primitive if the description is more specific than the modelling. Concept logical definition must not be more specific than concept description

LOINC uses time_aspect NPU is implied

Definition - Time of specimen collection

Must be stated consistently  in description AND modelling in accordance with SI editorial policy

modelling single point in time explicitly to enable correct classification of content

Time-specific concepts must not be subsumed by unmodelled soft default implicit 'single point in time' concepts

UK NRC to discuss applying the same principle

2

Inheres_in for sample based diagnostic reporting

All

Inheres_in effectively duplicates direct_site. They are two different perspectives (lab and clinical) of the same target

Direct_site is suitable for sample-based diagnostics and not other areas but NPU will not be following those guidlines

In Cancer Synoptic histology - carcinoma inheres_in neoplasm, when specimen is taken, the direct_site is specimen 

LOINC and NPU share linkage via 3 attributes, as SNOMED CT concepts they will classify as siblings, because of the different use of Inheres_in and direct_site

Can compute mapping using ECL

Some challenges e.g. NPU uses units, LOINC does not

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e.g. mass content of mercury in hair

mass content of iron in liver

Body structure is used for inheres_in for NPU-SNOMED CT project

This enables modelling location of hair from body structure hierarchy

also model cell structures - e.g. in erythrocytes 

use a specimen value of inheres in if the observable was specifically about the specimen (e.g. specimen volume).

ALL - Hair length can be another observation in FHIR observation group i.e. one observation to represent mass content of mercury in hair; and another observation to represent length of hair with a codable concept e.g. 12704-3 Length of hair

The mercury content inheres in the hair follicles were the hair structure was created and at the time when the structure was created.

the hair acts as a physical memory and integrator of mercury exposure https://www.annclinlabsci.org/content/36/3/248.full

Direct_site attribute sufficiently captures specimen and derivable substance / site from specimen modelling 

LOINC Ontology to model direct_site

NPU to model inheres_in

Create interoperable rules and document in guidance 

LOINC and NPU take different approached (to be documented)

UK NRC need to decide and test approach with LOINC Ontology content for UK gap requirements

3

Representation of percent

All

Concept is primitive if the description is more specific than the modelling. Concept logical definition must not be more specific than concept description

unit not required field in LOINC so in SNOMED CT, if fully defined without unit, could generate logical equivalences 

Represent percent in the description and the unit in SNOMED CT in accordance with SI editorial policy 

LOINC Committee decided to remove 100 denominator and reflect percent as UoM. LOINC Ontology will only release codes with 'fraction property (e.g number fraction, mass fraction)' and percent will be identified by unit.

Percent unit is used with NPU. NPU is more standardised with use of units so there is less variation (e.g. for substance conc, one unit)

International content will continue to model percent unit according to cancer synoptic content - any question mark for moving to LOINC Ontology?

UK will maintain SNOMED CT percentage subtypes to support the UK labs migration from Read, modelling percent unit as standardised exceptions, but align to LOINC Ontology properties in order to compute equivalences (when combined with unit %) and classify as subtypes if needed 

4

Inconsistencies - International content for cancer synoptic reporting by immunohistochemistry

1255078008 | Percent of cell nuclei positive for proliferation marker protein Ki-67 in primary malignant neoplasm by immunohistochemistry (observable entity) |

All

Does not use percent unit in modelling

e.g. 1 - modelling time_aspect -> single point in time but not stating this in the description

In contrast to LOINC Ontology examples that do state 'at single point in time' in the description and model in the logic

e.g.2 - use inheres_in whereas LOINC Ontology used direct_site

SI are adding percent unit to the content

Awaiting formal decision on inheres_in from this group

Awaiting formal decision on time_aspect from this group

5

Qualitative and semi-quantitative representation in SNOMED CT

KN

How do we represent both axes of ordinal AND qualitative / semi-q in SNOMED CT model?

NPU descriptions in this link (not complete yet): https://labterminology.com/npu-concept-model/general-rules-on-result-type/...

Hierarchies are inconsistent for qualifiers that represent the targets of scale_type defining attribute for observable entity concepts (see presentation slides)

Both are ordinal scales 

Both represented as presence in LOINC and international SNOMED CT

Semi-q needs to be defined

UK need to make a distinction between qualitative and semi-q in the terminology

6

Relative concentration of a substance in two different specimens

Relative concentration two different measurement properties

CALCULATIONS

KN / DK

How do we assess effort vs impact? The requirement to model them accurately for machine reasoning - auto-classifications; erroneous subsumptions

Karim reviewed the modelling options with Daniel and presented to group

Relative_conc_modelling options.pptx

Young Bae recommended we look at IUPAC relative properties and ratios

Patient test results calculations - consistent approach to reference external formulae, and not represent in SNOMED CT observable entity concept model (including ratios)

7

Fractions and ratios

After review of the resources, internal discussions and a review with the LOINC team, we've determined that "Ratio" and "Fraction" should be classified as sibling properties.

IFCC-IUPAC Silverbook https://iupac.org/what-we-do/books/silverbook/ but also on the homepage: https://labterminology.com/list-of-kinds-of-property/

NOTES

Mass content is deprecated in the IUPAC green book

Mass content and mass fraction are equivalent

No change required to SNOMED CT properties

NPU can map mass fraction to LOINC / SNOMED CT mass content

Mass fraction - of components (e.g. haemoglobin types)

Mass content - of the specimen (e.g. hair sample, calculus)

NPU is in agreement with LOINC for mass ratios and relative concentrations (mass or molar)

Expand ratios and relative concentrations in the terminology descriptions e.g.

Ratio of mass concentration of protein to substance concentration of creatinine in urine at point in time

Ratio of mass concentration of creatinine to mass concentration of protein in urine at point in time

Agreement to have sibling properties and not subtypes for fraction and ratio

Agreement on suggested terminology for FSN of ratios of different measurement properties and creation of new properties for mass/mol and mol/mass

8

Use of inheres_in for 

colour, appearance, identification

FA

inheres_in  used for the property to describe the characteristic of an organism, cell or body structure - applicable to LOINC Ontology representations

See Farazaneh's slides - 2025-04-08 - SI April Business Meeting Laboratory Terminology Standards WG - Room: Munch 2 - Laboratory reporting working group - SNOMED Confluence

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Microbiol0gy decisions

Placeholder - will summarise outputs once HL7 white paper is drafted