introduction to snomed ct - devdays.com … · introduction to snomed ct peter g. williams, snomed...
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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
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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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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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