Earlier this year, we attempted to standardise lab tests from two large regions of Scotland using SNOMED CT [within the UK, NHS England / NHS Digital Unified Test List #UTL]. Here is a summary of our experience. Check it out if you: ✅ Plan to consolidate your lab tests before a single LIMS procurement ✅ Aim to achieve cross-site working in a region while enabling lab data interoperability ✅ Intend to achieve conformance to the @NHSEngland Unified Test List This article also helps you understand how SNOMED CT (and the future NHS England standard UTL) might work in laboratory medicine. This is our presentation on this topic at the SNOMED International #SctExpo22 in Lisbon!

1. Experiences of
standardising
Lab Tests with
SNOMED CT
Jay Kola
CEO, Medical Informa6cian
29/09/2022

2. Termlex
• Team of ex-clinicians with long standing exper6se in clinical informa6cs
• Recognised interna6onally for exper6se in interoperability standards -
SNOMED CT, FHIR and openEHR
• Setup/supported Na.onal Release Centres (NRC) – Singapore, Sweden,
UK, Netherlands
• Exper6se in bespoke product development embedding APIs and
standards.
• Lead the development of England’s lab standards based on HL7 FHIR and
SNOMED CT. Specific exper6se in lab data, drug data, decision support
systems, data analy6cs
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3. Portfolio

4. Background

5. Why SNOMED CT?
• In England, lab standards mandated for use based on SNOMED CT, FHIR and
UCUM – aka not on LOINC
• Long history of use of Pathology Bounded Code List (~3,300 Read codes subset –
in primary care)
• The UK NRC publish the Unified Test List (UTL)
• ~4,200 SNOMED CT concepts (mostly results, ~400 requests)
• So ~3,800 are NEW SNOMED CT concepts for reporCng lab tests
• Other advantages of SNOMED CT
• UK successfully migrated their primary care systems (from Read) to SNOMED CT ~2018-19
• Single reference terminology for healthcare in the UK – primary, secondary, community care
• Can be used in more than blood sciences – Sarah Harry’s presentaCon
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6. Scope of the Work - Pilot
• Pilot project to create a single test catalogue across two large regions
(NHS Boards) in Scotland – Grampian and Lothian
• Pilot – so scope is not everything, but needs to cover mulBple
specialBes (blood science, microbiology, immunology)
• ObjecBves
• Create a single test catalogue of Lab tests
• Standardise lab reports: Convert HL V2 + uncoded è HL7 FHIR + SNOMED CT
• Iden6fy governance process + consensus based review
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7. Technical Overview
Grampian
Test List
Mapping – based on
review & consensus
Clinical
Data
Repository
Dra> Standardised
Test List
Standardised
Grampian Test List
with mappings
IntegraBon Engine
Lab
Reports
Transform Lab
reports, using
Mappings
Standardised
Lab Reports
Middleware Instance
Pathnexus Instance
Single Test List in
SNOMED CT RF2
format
Lothian
Test List
Standardised
Regional Test List
with mappings
LIMS
OrderComms
System
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8. Standardised Single Test List Creation
Local
Code
Local Description SNOMED CT Code SNOMED CT Term
FLALB Fluid Albumin 14101000237107
Albumin mass
concentration in fluid
HSTNI
Troponin I (High
Sensitivity)
1106481000000108
Cardiac troponin I mass
concentration in serum by
high sensitivity technique
DVH3 1,25-OH Vitamin D 30351000237105
1,25-Dihydroxy vitamin
D3 molar concentration in
serum
Local
Code
SNOMED CT Code SNOMED CT Term
BFALB Fluid Albumin 14101000237107
Albumin mass
concentration in fluid
BATROP HS Troponin I 1106481000000108
Cardiac troponin I mass
concentration in serum by
high sensitivity technique
BVITD1 1,25-OH Vit D 30351000237105
1,25-Dihydroxy vitamin D3
molar concentration in
serum
Test Id (SNOMED CT
Concept Id)
Standardised Test Name (SNOMED CT
Preferred Term)
14101000237107 Albumin mass concentration in fluid
1106481000000108
Cardiac troponin I mass concentration in
serum by high sensitivity technique
30351000237105
1,25-Dihydroxy vitamin D3 molar
concentration in serum
Standardised Single Test List
Site
A
Mappings
Site
B
Mappings
Import into LIMS, GP Systems, etc.
☑
☑
Pathnexify
⚡
Pathnexify
⚡
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9. Summary - Findings
• SNOMED CT works quite well for coding lab tests that are used in
both primary and secondary care!
• There is missing content in UTL and SNOMED CT – but this can be
addressed using post-coordinaBon!
• TransformaBon of HL7 V2 uncoded results to HL7 FHIR messages
works
• Mapping needs consensus!
• Governance process is key!!
Board Mapped
Requiring new
concepts
Unable to map
Grampian 344 21
Mostly due to scope
issues
Lothian 192 7
Mostly due to scope
issues
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10. Findings - Discussion

11. Mapping can be tricky- SemanDcs
● In the lab world, you have to deal with:
○ Level of granularity
○ Aim for the exact equivalent for your lab se]ng
○ Rely on SNOMED CT to `group` things
● Is this a request vs result
F1BC Fibrinogen Level
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12. Mapping – Specimens
● In the lab world, you have to deal with:
○ Specimens that are significant: `skin lesion` vs `nasopharyngeal swab`
○ Specimens can be interchangeable across sites – legi6mately!!
■ `Serum` vs `Plasma`
○ Rely on the lab specialist to determine if specimens are interchangeable!
● RaBonale for governance!!
FSH1 FSH
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13. Mapping – Specimens (2)
● Specimen affects `comparability` of tests!!
● What if the specimen disBncBon isn’t’ required?
○ Don’t worry - SNOMED CT s6ll works 😬
○ Exis6ng SNOMED CT content
■ 762634006 |Acellular blood (substance)|
■ 788707000 |Plasma specimen or serum specimen or whole blood specimen (specimen)|
■ 119297000 |Blood specimen (specimen)|
○ You can always use `post-coordina6on`!!
● Remember – use SNOMED CT to `group` these post-hoc (a[er mapping)
● Not all these concepts are fully defined – can catch you out at post-hoc
querying
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14. Mapping – Right EdiDon
● SNOMED CT content is layered in a sense:
○ UK PaLM (UTL)
○ UK Clinical Edition
○ International edition
● Determining Relevance
○ `Learning`
○ Order of extensions
○ National > International?

15. Mapping – Missing Content
● UTL / SNOMED CT does not cover everything
○ Does any code system ever have everything?
○ How many `monkeypox` test codes existed before 2022?
● What do `users` do when `their test` is missing?
○ Request new code from NRC? 🤷‍‍
○ Can we allow users to create `standardised tests on the fly` without being
SNOMED CT experts? 😱
● These needs exist in the world…
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16. Mapping – Missing Content (2)
● These are examples that we found in our work
○ High sensi6vity tests for Troponins I and T
○ Technique hierarchy needs expanding
● So we ended up creaBng fully defined tests for:
○ Cardiac troponin T mass concentra6on in serum by high sensi6vity technique
○ Cardiac troponin T mass concentra6on in serum by high sensi6vity technique 😱
● If so – how?
○ Post-coordina6on to the rescue (but can be pushed)
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17. Post coordinaDon – Lab tests
Test for `Amiodarone Mass Concentration in acellular specimen`
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18. Post coordinaDon – Lab tests (2)
● Why bother with post-coordinating lab tests
○ Allows creation of tests that don’t exist
○ Diagnostics is a rapidly exploding!
○ Allows analysis of data using SNOMED CT (ad-hoc), even if it is coded in other
coding systems (e.g. LOINC – interoperation)
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19. Post coordinaDon – Lab tests (3)
● Here is what happens when
you do this with Microbiology
○ Colony counts, suscep6bility
and more
● Be sane about `terminology
model` vs `informaBon model`
balance!!
● Pick where you want to `post-
coordinate`!
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20. Mapping - Requests
● SNOMED CT works quite well in the lab requests space – historical
● Panels – high level content exists ✅
● DefiniBon of panels ☹ but LOINC ✅
● LocalisaBon of Panels in neither ☹
● Some tricky UK specific issues in UTL
PORFR Faecal Porhyrins
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21. Summary
● It is possible to standardise lab results and requests using SNOMED CT
○ Works for blood sciences and other domains
● Need for new content exists in SNOMED CT
○ Need for new test crea6on exists across the diagnos6cs domain
○ Post-coordina6on can be used to create `new tests`
● EffecBve use of post-coordinaBon can allow true lab interoperability –
best of both worlds in SNOMED CT and LOINC (LIVD, UCUM, etc)
● Not covered but equally interesBng – implementaBon challenges,
transformaBon of messages, analyBcs
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22. Want to know how
Pathnexus can work
for you?
www.pathnexus.com
info@termlex.com

23. Contacts &
Acknowledg
ements
• We would like to acknowledge
• NHS Digital for their excellent work on the
Unified Test List (aka SNOMED CT for Lab)
• NHS Grampian and NHS Lothian trusts for
sharing their test catalogues
• NHS Scotland for the PoC work
Jay Kola – jay@termlex.com
Sarah Harry – sarah@termlex.com
General info: info@termlex.com

24. Thank you – Questions?
Want to discuss more? Email info@termlex.com