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Introduction to SNOMED CT

Peter G. Williams, SNOMED International

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Introduction to SNOMED CT

• What is SNOMED CT and why is it great?• SNOMED CT’s Logical Structure• Expression Constraint Language (ECL)• SNOMED Reference Sets• Snowstorm Terminology Server• How to best use SNOMED CT with FHIR

• CodeSystem• ValueSet• ConceptMap

• SNOMED on FHIR Working Group

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What is SNOMED CT ?

• The most comprehensive & precise clinical terminology in the world• Structured & controlled clinical vocabulary• Ontology, directed acyclic graph, polyhierarchy• Self describing

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Why is SNOMED CT great?

Comprehensive

Computable

Variable granularity

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A brief history of SNOMED CT

• College of American Pathologists (CAP - US)• 1965 Systematized Nomenclature of Pathology (SNOP)

• 1974 SNOMED -> 1979 SNOMED II -> 1993 SNOMED 3 -> 1998 SNOMED 3.5

• National Health Service (NHS - UK)

• 1986 James Read (v1 4-bytes) -> 1991 v2 (5-byte) -> 1998 Clinical Terms Version 3

• 2001 CTV3 + SNOMED RT -> SNOMED CT (2002)

• 2007 International Health Terminology Standards Development Organization

• 9 charter member countries acquired rights from CAP

• 2017 IHTSDO changes name to SNOMED International

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SNOMED CT’s Logical Structure

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• Concepts are the central components of SNOMED CT

• A SNOMED CT Concept is a clinical idea associated with a unique identifier

• The meaning is specified by an association with a term known as the fully specified name (FSN)

• The link between the identifier and the meaning of that clinical idea is permanent and unchangeable

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Descriptions• Each concept is associated with several descriptions• A description links a human-readable term to a concept

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Relationships

• Concept triple - source, type, target

• Express defining characteristics & can be grouped together

SNOMED CT Concept

Appendectomy

Procedure

Procedure by site

Procedure on body system

Procedure by method

Procedure on digestive system

Surgical procedureRemoval

Surgical removalProcedure on digestive

tract

Operative procedure on digestive system

Procedure on trunk Procedure on organ

Operation on digestive tract

Procedure on digestive organ

Procedure on abdomen

Operation on trunk

Procedure on gastrointestinal tract

Excision

Operative procedure on digestive organ

Procedure on intestineOperation on

abdominal regionOperation on

gastrointestinal tractTrunk excision

Operation on intestineLower gastrointestinal

procedureProcedure on large

intestineAbdomen excision

Excision of intestinal structure

Operative procedure on large intestine

Procedure on appendixLarge intestine

excision

Partial excision of large intestine

Operation on appendix

IS A - Polyhierarchy

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Attributes

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Expression Constraint Language (ECL)

Symbol Meaning

< Descendants Of

<< Descendants and Self

: Where

^ Member Of

* Any

MINUS, AND, OR, ( ) Logical Operations

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ECL Example

< 763158003 |Medicinal product (product)| :

<< 762951001 |Has ingredient (attribute)| =

255641001 |Caffeine (substance)|,

732946004 |Has presentation strength denominator

value (attribute)| = *

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ECL Example ++

( < 763158003 |Medicinal product (product)| :

<< 762951001 |Has ingredient (attribute)| =

255641001 |Caffeine (substance)|,

732946004 |Has presentation strength denominator

value (attribute)| = * )

AND ^ 123456709 |UK Restricted Drugs|

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SNOMED CT Reference Sets

• Simple Refset (subset, valueset)

• Simple Map• Attribute Value Refset

• Association Refset

• Language Refset

• Complex Map (extra rules eg ICD-10)

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The Snowstorm Teminology Server

• https://github.com/IHTSDO/snowstorm

• Build initially for SI’s Authoring and Browser Applications

• Scalable storage using Elasticsearch

• Platform agnostic Java implementation

• Open source Apache 2.0 license

However, Snowstorm:

• is not commercially supported by SNOMED International• only supports SNOMED CT, not other terminologies

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Using SNOMED CT with FHIR (and Snowstorm)

• Terminology Resources with Operations particular to SNOMED CT

CodeSystem ValueSet ConceptMap

$lookup Implicit valuesets $translate

$validate-code $validate-code

$subsumes $expand

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CodeSystem - instances & searching

https://temp-snowstorm.ihtsdotools.org/fhir/CodeSystem

.../CodeSystem?version=20190731

.../CodeSystem?publisher:contains=SNOMED

Example:

.../fhir/CodeSystem/sct_11000181102_20191130MODULE SCTID EFFECTIVE DATE

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CodeSystem - $lookup

https://temp-snowstorm.ihtsdotools.org/fhir/CodeSystem/$lookup?

system=http://snomed.info/sct&code=840539006

.../CodeSystem/$lookup?code=840539006&

version=http://snomed.info/sct/900000000000207008/version/20190731

.../CodeSystem/$lookup?code=322236009&property=normalForm

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CodeSystem - $validate

https://temp-snowstorm.ihtsdotools.org/fhir/CodeSystem/$validate-code?

coding=http://snomed.info/sct|32553006

.../CodeSystem/$validate-code?coding=http://snomed.info/sct|32553006&display=nausea

.../CodeSystem/$validate-code?code=443971000124108

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CodeSystem - $subsumes

Check if 399144008 |Bronze diabetes (disorder)| is a type of 73211009 |Diabetes mellitus (disorder)|

.../CodeSystem/$subsumes?codeA=399144008&codeB=73211009

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ValueSet- instances & searching

https://temp-snowstorm.ihtsdotools.org/fhir/ValueSet

https://temp-snowstorm.ihtsdotools.org/fhir/ValueSet?title:contains=condition

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ValueSet - $expand

https://temp-snowstorm.ihtsdotools.org/fhir/

ValueSet/allergyintolerance-code/$expand?

force-system-version=http://snomed.info/sct/11000146104

&displayLanguage=nl&

filter=pollen

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Implicit ValueSet

Procedures on the heart

<< 362958002 |Procedure by site (procedure)| :

<< 363704007 |Procedure site (attribute)| = 80891009 |Heart structure (body structure)|

.../ValueSet/$expand?url=http://snomed.info/sct?fhir_vs=

ecl/<<362958002:<<363704007=<<80891009

.../ValueSet/$expand?url=http://snomed.info/sct?fhir_vs=

ecl/<<362958002:<<363704007=<<80891009&

filter=MRI

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ValueSet - $validate-code

Is this code part of my ValueSet and is the correct display term used?

.../ValueSet/$validate-code?

url=http://snomed.info/sct/900000000000207008/version/20200309?fhir_vs=ecl/<<34014006|Viral+disease|&

coding=http://snomed.info/sct|840539006

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ConceptMap - $translate

.../ConceptMap/$translate?code=254153009&

system=http://snomed.info/sct&

source=http://snomed.info/sct?fhir_vs&

target=http://hl7.org/fhir/sid/icd-10&

url=http://snomed.info/sct?fhir_cm=447562003

.../ConceptMap/$translate?code=134811001&

system=http://snomed.info/sct&

source=http://snomed.info/sct?fhir_vs&

target=http://snomed.info/sct?fhir_vs&

url=http://snomed.info/sct?fhir_cm=900000000000527005

ICD-10 Map target for 254153009

|Familial expansile osteolysis

(disorder)|

Historical Association find the "SAME

AS" target for inactivated concept

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ConceptMap - $translate is dangerous in reverse

.../ConceptMap/$translate?code=Q79.8&

system=http://hl7.org/fhir/sid/icd-10&

source=http://hl7.org/fhir/sid/icd-10&

target=http://snomed.info/sct

Q79.8

Other congenital malformations of

musculoskeletal system

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Using ECL with Term Filtering in an Application

http://snomed.org/ui

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SNOMED on FHIR Workgroup

● Created Wellington, NZ Oct 2016 ○ At request of members○ Intended to support FHIR implementation specifically using SCT

● Every Tuesday evening 20:00 UTC● HL7 and SI on equal footing - Rob Hausam co-chair● Two streams of work (week about)

○ Terminology Services■ Michael Lawley (CSIRO), Peter Jordan (HL7 NZ)

○ Terminology Binding■ Jeremy Rogers (NHS Digital), Daniel Karlsson

https://confluence.ihtsdotools.org/display/FHIR/SNOMED+on+FHIR

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Questions?

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