2025-06-25 - Laboratory Terminology Standards WG Meeting

1

Inheres_in 

ratios, fractions, mass content

Question from UK NRC to the NPU to SNOMED CT translation project:

Should Inheres_in be to substance or body structure for anatomy?

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Daniel - not in our Top 100 list, but we do have body structures though, as cell structures (leukocytes etc.) are body structures. We would I guess only use a specimen value of inheres in if the observable was specifically about the specimen (e.g. specimen volume).

I would assume that the first one would inhere in the liver, for the second one there is both 395508003 |Hair - material (substance)| and 386045008 |Hair structure (body structure)| to consider. 119326000 |Hair specimen (specimen)| is defined by the body structure.

A (patient) system is an “arbitrarily defined part of the universe” and the domain of “Inheres in” is any material entity (substance, organism, body structure, physical object, … in SNOMED CT) so the two are aligned (by design).

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

The current NPU concept: NPU02700, Hair—Mercury; subst.cont. = ? µmol/kg does not capture that meaning.

perhaps in the information model and not in the code. The FHIR resource currently does not support this though.

Gunnar - The mercury content inheres in the hair follicles were the hair structure was created and at the time when the structure was created. This timepoint differ from the sampling time of the hair. This is utilized clinically; the mercury content of the hair might thus reflect the mercury challenge for the body one or more months prior to the sampling (depending on the hair cut + distance from scalp

The sampling is probably standardized in some way – we have to ask the experts. And this standardization ought to be included in the code.

Young Bae - 

Agree on the information is needed but in the common laboratory information model. Not in the description of the quantity.

 Check if we can represent hair length in FHIR Body Structure resource.

Presentation from Andrew / Gunnar on properties - mass fraction vs mass content; substance conc ratios etc

 2

Post-coordination in information model proposals

Lab semantic WG meeting in Prague program 6.-7. July 2025

grouping / panels - FHIR R6 'organizer' element in Observation profile

microbiology structured data

value sets

Stan Huff's slides:

Follow up with EU group, Rob's group - how do we work to the same standard blueprint to design the structured model-terminology

Update: Hynek has arranged hybrid event in Prague - 6th and 7th July

Question to Rob - present Organiser data element?

Question to LOINC designers - Shall we try to co-present and highlight the overlaps in the information model-terminology design proposals? 

3

new attribute in the Specimen hierarchy of “Specimen adjustment (attribute)" 

Suzanne (Farzaneh, Jim or Stan)

We have got further information from the LOINC team, which may affect the decision regarding creating an attribute.

has text definition of “Identifies the adjustment made to a specimen.”

We would appreciate the input from this group on the proposed new attribute and if it should be added to the international release. This would of course require an MRCM change. It is expected that changes will be made in LOINC, e.g., to move “adjustment to ph 7.4” from being a subpart of the Component to be a sub-part of the System.

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based on the number of affected LOINC terms (very few) adding a new attribute seems a bit of an overreach at this point. The options we are considering:

1. either creating specimen concepts where adjustments are specified in the FSN

2. or to leave the LOINC terms (all leaf level) as primitive.

4

Amphetamine+analogue in NPU 

Daniel

When mapping NPU elements to SCT, question:

SCT 412035000 | Amfetamine and/or amfetamine derivative (substance) |. We looked also into the LOINC mapping and found that the same concept was used to map from Amphetamines (with a definition from MeSH reading “Analogs or derivativs of amphetamine…”). Analog is not the exact same thing as derivative. We seem to share the same concept in LOINC and NPU (to no surprise…). How do we proceed?

UK NRC - unclear on exactly what amphetamine analogue is

At least according to Wikipedia they probably do fall under the concept 412035000 |Amfetamine and/or amfetamine derivative (substance)|

Substituted amphetamines, or simply amphetamines, are a class of compounds based upon the amphetamine structure;^[1] it includes all derivative compounds which are formed by replacing, or substituting, one or more hydrogen atoms in the amphetamine core structure with substituents

Is it the sort of things that cause false positives?

“false-positive amphetamine urine drug screen include fluoxetine, selegiline, ranitidine, trazodone, nefazodone, brompheniramine, phenylpropanolamine, chlorpromazine, promethazine, ephedrine, methamphetamine, and labetalol”

FA - analogue is discouraged in SNOMED CT. It is ambiguous because these can be structural or functional analogues, can be similar structure but no a direct chemical derivation of the compound.

GN - NPU should discourage use of analogue terming too, unless 'structural analogue' is specified e.g. ecstasy as the structural analogue of amphetamine

DK - so the naming of the source concept in NPU should be addressed and it's not a SNOMED issue 

SH - there is a concept for amphetamines, the class of substances, and then singular amphetamine to test for the pure substance

NPU folk to take back and clarify the source terminology representation.

Update - structural analogues and derivatives can be considered synonyms, as such can be mapped from NPU which uses structural analogues. 

This can be closed 

AOB

1

International decision for sharing and reusing path and lab SNOMED CT observable entity content

2

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

3

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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5

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

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 approach

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/

Agreement to have sibling properties and not subtypes