0 an Introduction to SNOMED CT1

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SNOMED CT& HL7 TERMINOLOGY BINDr. Abbas Shojaee BUMS, June 2010

This presentation uses works of:1. Tim Benson2. Ian Horrocks3. Kent A. Spackman


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Vocabulary

Syntactic: Semantic:

Lexical:

Homonym:

Synonym:


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Presentation

What is interoperability?What is SNOMED CT?Uses of SNOMED CTSNOMED Standard Development Organisation (S

- Why the change/why join?- What is the current situation?

The role of WHOConclusions


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Definition


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SNOMED CT5

The Systematized Nomenclature Medicine Clinical Terms


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6

SNOMED CT

SNOMED Clinical Terms (SNOMED CT) is a dynamic, scientificallyvalidated clinical health care terminology and infrastructure that makeshealth care knowledge more usable and accessible. The SNOMED CTCore terminology provides a common language that enables aconsistent way of capturing, sharing and aggregating health dataacross specialties and sites of care. Among the applications for

SNOMED CT are electronic medical records, ICU monitoring, clinicaldecision support, medical research studies, clinical trials, computerizedphysician order entry, disease surveillance, image indexing andconsumer health information services.

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Motivation


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Why SNOMED CT might be of my in

Archimedes: Give me a place to stand anda lever long enough and I will move the woThis lever to mathematicians is Numbers, thepercept and move the world through numbersThis lever to medical knowledge and informaworkers, is going to appear in SNOMED CT successors.
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ORIGIN and HISTORY

SNOMED CT


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SNOMED

SNOMED International:The division of the College of American Patholresponsible for maintenance and release of

SNOMED CTSNOMED CT

Releases twice yearly (January & July) of theterminology commonly called SNOMED
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Development of terminologies

SNOP

SNOMED 2

SNOMEDRT

SNOMED CT

Read 4 byte

READ 2

READ 3 (CTV3)

SNOMED 3

SNOMED R d C d
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SNOMED CTV3 Timelines

SNOMED Read Codes

SNOMED 2 1979 - 19821983 Read Codes (v1)198419851986

19871988 Professional Endorsement19891990 Purchased by NHS19911992 Clinical Terms Projects

SNOMED 3 1993 , 1994 1995 CTV3 (Clinical Terms version 3)

1996 UK Govt Inquiries into Read CodesCAP business plan 1997

1998 NHS Agreement 1999 CAP Agreement

SNOMED RT 20002001

2002SNOMED Clinical Terms

Formation of theSNOMED

International Divisionof the C.A.P.
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SNOMED HistorySNOP 1965 basis for ICD-OSNOMED 1974SNOMED II 1979SNOMED Version 3.0 1993SNOMED Version 3.5 1998SNOMED RT 2000 (Merge with UK NHS)

SNOMED CT(SNOMED RT + CTV3) 2002SNOMED CT Spanish Edition April 2002SNOMED CT German Edition - April 2003Free in USA - Agreement with NLM June 2003SNOMED SDO Proposal 2006
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User distribution - SNOMED CTAustralia Hungary New Zealand Sweden

Austria Iceland Norway Switzerlan

Belgium Iran Oman Taiwan

Canada Ireland Poland Thailand

China Israel Portugal Turkey

Denmark Italy South Korea U.A.E.

Estonia Japan Saudi Arabia United Kin

Finland Malaysia Singapore United Stat

France Namibia South Africa

Germany Netherlands Spain
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What is SNOMED CT

Essence


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What is it?A reference terminologyA clinical terminology

with reference and interface properties

A CD containing a set of tablesA set of codes with namesA set of definitions per genus et differentiam

A clinical terminology standardA knowledge base?A dictionary?An ontology?An application ontology?
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Formal Ontology?SNOMED is not a formal ontology (but some parts of it are migrating in thatIt is a reference terminology that is progressively more well-supported by forontological principles

Includes terms and non-ontological assertions / ideasI dislike the term application ontology fish or fowl?

Many of SNOMEDs design decisions are supported by formal ontological principles.But

Many of SNOMEDs hierarchies are still unprincipled and incomplete.

Requires continued evolution and maturation
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What is an Ontology?


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A model of (some aspect of) the world


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A model of (some aspect of) the worldIntroduces vocabularyrelevant to domain, e.g.:

Anatomy
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AnatomyCellular biology


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AnatomyCellular biologyAerospace
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Anatomy

Cellular biologyAerospaceDogs


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AnatomyCellular biology

AerospaceDogsHotdogs
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What is a Clinical Terminology?

Ordinarily:A finite enumerated set of terms intended to coninformation unambiguously

SNOMED is more than thisTerms plus codes plus the ability to put them togmeaningful ways


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What is SNOMED CT?A work of clinical terminology for coding, retrievinanalyzing data about health and health careComprised of codes, terms and relationships, for usprecisely recording and representing clinical informacross the scope of health careConcept-based: Each code represents a single meanand can have multiple descriptions (terms)
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What is notSNOMED is not the language police

Clinicians determine what words mean by how they use SNOMED reflects those meanings.

SNOMED is not an independent source of scientific/profespractice standards

Scientists and professional groups define their standardsto follow those standards.

SNOMED is not a comprehensive knowledge base for healtThis is out of scope. SNOMEDs goal is terminological knthat which is always necessarily true of a term.


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What does it do?

SNOMED CT is a terminological resource thbe implemented in software applications torepresent clinically relevant information

In a semantically structured form that can be used bautomated applications
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What is it for?

It is for building applications capable of:Recording statements about the health and healtof individuals

In a way that permits retrieval according to the meathe statements, rather than just the words used

Retrieving individual cases and groups of casesTo enable more automated and sophisticated decisisupport, epidemiology, and research


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Pictures can also be presented more dramatically in widescreen.

Desiderata for a global terminology

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1. Comprehensiveness:Coverage for all aspects of health care

2. Adequacy:Is it fit or purpose multiple purposes?Does it have a good information model and ontological basis?

3. Multilingual applicabilitylanguage independent formal concept representationRepresentation in multiple languages more than translation

4. Utility:Is it beneficial for:

Care providers : decision making, outcome evaluationConsumers : participation ownership evaluation risk reductionPolicy/Decision Makers : informed decision making on costs, benefits, efficiency

5. Reliability:does it give the same results in different users

Source: T. Ustun, WHO, SNOMED Semantic Mining Conference, Copenhagen, Oct. 2006
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Desiderata for a global terminolog

5. Validity:5. Does it indicate the right things and does the indication make sense

6. Comparability

5. Does the data in different context have same properties to be compared

7. Interoperability

5. Technical: Can information systems exchange information and use it?

6. Semantic: Can information systems interpret the data with the same meaning?

8. Quality Assurance5. Product : Annotation and Content

6. Process : Use and Usability

9. Sustainability

5. Secured maintenance: commitment to stability with earlier versions

6. Openness to address emerging technical issues

Source: T. Ustun, WHO, SNOMED Semantic Mining Conference, Copenhagen, Oct. 2006
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SNOMED CT Structure

HierarchiesParent child relationshipsVertical structureConcepts may have multiple parents

Relationships between conceptsUsing attributes, concepts may be linked to eachHorizontal relationships
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Healthcare systems includedICD9-CMICD-V2-OncologyLOINCOphthalmology-relatedterms

Systematized Nomenclatureof DentistrySM of Vet Med

NANDA Taxonomy

Nursing InterventioClassification

Nursing Outcomes

Peri-operative Nursi

The Omaha SystemThe Georgetown HoCare Classification
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SNOMED CT Structural compon

SNOMED CT is composed of components, winclude concepts , relationships , descriptionssubsets , and cross maps ,Each of which is identified by a SNOMED CIdentifier (SCTID) and has a validity status.
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Components of SNOMED CTConcepts

The basic units of SNOMED CT

DescriptionsThese relate terms that name the concepts to the concepts themselves. Each concept has at least two Description

HierarchiesConcepts are organized into twenty SNOMED CT hierarchies (in UK extension). Each hierarchy has sub-hierar

Relationships

Relationships are the connections between concepts in SNOMED CT.

+ mappingsMany-to-many mappings to terms in ICD and OPCS

+ Inclusion of Dictionary of Medicines and Devices
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SNOMED Clinical Terms Identifier (S

The SCTID is a 64 bit integer- between 6 anddigits long.All components are identified using a special
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Validity StatusAn important principle of SNOMED CT is that permanence.Once a component such as a concept or descriptbeen created it is never deletedStatus codes:

Active: Current (0), Limited (6), Pending move (11Inactive: Retired (1), Duplicate (2), Obsolete (3), A(4), Erroneous (5),Inappropriate (7), Inactive concepImplied (9), Moved elsewhere (10)


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Concepts

SNOMED CT is concept-orientedA concept is just a clinical idea to which a unConceptID that is a SCTIDConcepts are formally defined in terms of therelationships with other concepts:

Subtype relationship: Concept Z IS_A concept YAttribute relationship

C t t f SNOMED CT O i d i 19 diff t hi


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Content of SNOMED CT: Organized in 19 different hieraThese are indeed high level concepts

SNOMED CT : Root conceptClinical FindingProcedureObservable entityBody structureOrganismSubstancePharmaceutical/biology productSpecimenPhysical objectPhysical force

EventsEnvironments/GeolocationsSocial ContextContext-dependentStaging and scalesAttributeQualifier valueSpecial concept

Concept Example
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Concept ExampleGastric ulcer (SCTID397825006)

Terms:

Gastric ulcer (disorder)Gastric ulcerStomach ulcerGU Gastric ulcerGastric ulceration

Relationships:Is_a Disease of stomachIs_a Gastrointestinal ulcer

Associated morphology UlcerFinding site Stomach
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DescriptionsEach description has a DescriptionID which is a SCTIEach description links a human-readable term with a cEvery concept has at least two descriptions:

Fully specified name (FSN) : is a phrase that names a concway that is both unique and unambiguous

Preferred term : the common phrase or word used by clininame a conceptEach concept may have several other descriptions: e.g.synonyms, translations
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RelationshipsRelationships are at the heart of SNOMED.More than 1.3 millionEach relationship is defined as an object-attribute-value

The object is the source concept (the one that has the relations(ConceptID1).The attribute specified the type of relationship and is also a SCT concept.The value is the target.

Concept: attribute = value (e.g. Gastric ulcer (SCTID397825006) Is_astomach)
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SNOMED CTComponents


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SNOMED Clinical Terms Identifier

A 64 bit integer -between 6 and 18digits long.
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SNOMED CTHierarchies


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Lets bypass the restSNOMED CT struc
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SNOMED CT ExpressionsClinical records are created for the purpose of providinformation about events or states of affairs.A SNOMED CT expression is a collection of referenone or more concepts used to express an instance of clinical idea.

pre-coordinated a single concept identifier is used to ra clinical ideaPost-coordination representation of a clinical meusing a combination of two or more codes


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SNOMED CT expression


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Documentation

U G id


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SNOMED CT Documentation:User GuideExplains the content and the principles used to model tterminology.Intend: To explain SNOMED CTs capabilities and uses fromcontent perspective.Audience: clinical personnel, business directors, softwproduct managers, and project leaders; informationtechnology experience, though not necessary, can be he
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SNOMED CT Documentation:Technical Reference Guid

Contains reference material related to the current releaSNOMED CT and includes file layouts, field sizes, reqvalues and their meanings, and high-level data diagramAudience: for SNOMED CT implementers, such as sodevelopers. assumes an information technology backgrclinical knowledge is not a prerequisite.


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SNOMED CT Documentation:Technical Implementation Gu

Contains guidelines and advice about the design ofapplications, terminology services, entering and storininformation, and migration of legacy information.Audience: for SNOMED CT implementers, such as sodesigners. assumes information technology and softwadevelopment experience. Clinical knowledge is not reqalthough some background is helpful to understand theapplication context and needs


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CLINI Clue

BROWSER


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PulmonaryTuberculosis

kind of Puldisease dueMycobacter

kindtube

kind ofpneumon

found in lungstructure

caused byMycobacteriumtuberculosis complex


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Employing SNOMED CT

Wh t b t li i l d i i


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What about clinical decision supIF Two blood cultures, drawn throan antibiotic removal device, mor

than 30 minutes apart,

grow no organism,THEN discontinue antibiotic.

procedures
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IF Two blood cultures , drawnan antibiotic removal device , m

than 30 minutes apart ,

grow no organism ,THEN discontinue antibiotic .device

Clinical Decision Support Model+ Inference Rules


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+ Inference Rules

Terminology Model+ Coded Data

Informat+ Patient Da

Diagram based on Figure 1 in Rector AL et al. Interface of

Clinical Decision Support Model+ Inference Rules


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+ Inference Rules

Terminology Model+ Coded Data

Informat+ Patient Da

IF Two blood culturesAntibiotic removal devicthan 30 minutes apart ,THEN discontinue antib

30088009 blood culture55512120 antibiotic removal device264868006 No growth281789004 antibiotic therapy223438000 advice to discontinue a procedure

What test was perfoHow many were doAt what time?What device was usWhat was the result

Diagram based on Figure 1 in Rector AL et al. Interface of

SNOMED CT

Using SNOMED CT and HL7 to
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Using SNOMED CT and HL7 towe cannot separate the issues of informationstructure from those of terminology.We cannot slot any terminology into any datastructure and expect it to work.

SNOMED CT was designed to be syntax-neuit could work with any syntax.HL7 RIM and set out to be terminology-neut
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Benefits of

Interoperability


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InteroperabilityIn the context of e-health, interoperability is tway in which reliable data is provided andcommunicated in a secure, accurate and efficway. It has to surmount the barriers of nationapolicies, culture, language and systems of meknowledge representation and use of ICTs.Towards Interoperable eHealth for Europe. Telemedicine Alliance. BR255November 2005

Classifying and Coding hi h i


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Classifying and Coding, which is more Coding means understanding?

Assigning codes to concepts.Identifying the concepts.Clarifying them.

Dealing with homonyms, synonyms and overlapsEnables us to identify and document interrelationshThis is indeed


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SNOMED CT is the most comprehensive, multilingual clin

healthcare terminology in the world.The value of SNOMED CT can only be realized when it is software and systems that are designed around itKent Spackman:

The first rule of data quality is that the quality of data collecte

directly proportional to the care with which options are presenuser.The first rule of coding is that yesterdays data should be usable today

SNOMED CTat 2009


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SNOMED CTat 2009SNOMED Reference Terminology Clinical Terms Version 3310,000 health care concepts990,000 synonyms and English descriptions1.38 million semantic relationships

ICD 10 containconcepts comin

large volum

Content Content Content


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Number of Concept Codes

10,990 30,54796,042

128,030

0

50,000

100,000

150,000

200,000

250,000

300,000

350,000

SNOP1965

SNM21979

SNM31993

SRT2000

Edition of SNOMED

Content, Content, Content

Standardized Healthcare Langua
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Standardized Healthcare LanguaNeed for a normalized healthcare vocabulary.Across settings, applications, datasets.SNOMED CT, UMLS.
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Problems of SNOMED CT

concept codes that are fullydefined
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defined

0%

5%

10%

15%

20%

25%

30%

Tot Dis Find Proc Other

Eventually should reach ~70% or more of disorders, findings & pro

Error types - 1


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7202.10.2006

Gergely Hja -SMCS2006

Error types 1Misplacing concepts in the hierarchy

smoker (an agent ) is subsumed by tobacco smoking bfinding (a role )severe asthma is not a kind of asthma, but a kindfinding .

Mixing the subsumption relation with other rolespart of)

haemoglobin subsumes haemin (instead of constitutionaexacerbation of asthma attack is subsumed by asthmatemporal part)

Error types - 2


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7302.10.2006


Error types 2Hierarchy violating medical thinking and biknowledge

Disease , observation and finding are subsumedfinding

acute on chronic , which is both subsumed bychronic

polycarbonate is a polymer ( instead of synthetic po

Error types - 3
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7402.10.2006


ypContracting disjoint entities into one concept

Smoker (an agent ) and smoker (finding) (a description ofadditional pathologic finding in tumor specimen (observable entadditional pathologic findingFunction is classified as an observable entity

Ontological definition: ability of an object to play a certain role in aactivityfunctions (e.g. gene function, adaptation )

measures (quality ) that evaluate the realisation of a function (e.g. rexcretory rate )Inflammation (morphological abnormality) (a physicalinflammatory reaction (perdurant )

Additional problems - 1
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Additional problems 1Categories taken form classification systems

pneumonia in other diseases classified elsewhere (markeConceptStatus Limited)The danger of taking over concepts from other conceptusystems: the context of the concept is lost. What is meanother diseases classified elsewhere ?

relations (such as part of ) are represented also asconceptsIt prohibits the direct conversion to any formalism basedorder logic, thus to any DL formalism

Additional problems - 2
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7602.10.2006


Additional problems 2Underspecification:

roles are not quantified (existential / universal)criteria are not specified (necessary / sufficient)conversion to DL: do we have to decide in each particular cit be done universally?

Multiple hierarchyalcoholic beverage (through its parent ingestible alcohol ) is subsume

depressant , ethyl alcohol and psychoactive substance of abuse

nonpharmaceutical. Alcoholic drinks contain ethyl alcohol, which plays depressant and substance of abuse (with respect to human beings)Is this a general phenomenon in SNOMED?Which relations are asserted and which are inferred?

Discussion - 1


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D scuss oThe intended meaning of the categories is noalways clear: possible translation errorsIs it reasonable to import categories from meclassifications?

SizeArtificial conceptsConsistency errors

Discussion - 2


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7802.10.2006


Real world entities listed heterogeneouslyMars bar and Kit Kat (chocolate candy would sUFO is subsumed by transport vehicletendon pulley reconstruction is represented, but

pulley not

Solutions


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02.10.2006Gergely Hja - SMCS2006

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Use SNOMED as a plain or loosely structurterms (with extending the coverageappropriate for intelligent services.Restructure SNOMED into a high-quality onBuild a new medical ontology from scratchreuse of the existing ones), and to restrict thSNOMED for interoperability by mapping cto it.

Restructuring SNOMED


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g

02.10.2006Gergely Hja - SMCS2006

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A formal top level ontology (e.g. DOLCE).

A high level core reference ontology of general medknowledge (e.g. anatomy, physiology, pathology, meprocedures).

Logic-based formalismSingle hierarchies with formal definitions

(sub)domain ontologies of specialitiesCompound entities (e.g. tonsillitis)Manual assertion (e.g. autism)
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Future Researches

Some Research Challenges


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gExtend saturation-based techniques to non-Horfragments

SNOMED users want negation and/or disjunctionNon infectious PneumoniaInfectious or Malignant disorder of lungBurn injury of face neck or scalp

Extend reasoning supportModularityExplanation...

Some (more) Research Challenges


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( ) gOpen questions w.r.t. query rewriting

FO rewritability (AC0) only for very weak ontology langEven for AC0 languages, queries can get very large (orde

), and existing RDBMSs may behave poorlLarger fragments require (at least) Datalog engines and/extension to technique (e.g., partial materialisation)

Integrating DL/DB researchOntologies -v- dependenciesOpen world -v- closed world

Widescreen Test Pattern (16:9)
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Aspect Ratio Test

(Should appearcircular)

16x9

4x3

SNOMED CT hierarchy


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Why Care About Semantics?


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Why should I care about semantics?



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Well, from a philosophical POV, wspecify the relationship between statelogic and the existential phenomena th




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Well, from a philosophical POV, wspecify the relationship between statelogic and the existential phenomena th

Thats OK, but I dont get paid for philosophy.



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In FOL we define the semantics in terms of models (a model theory). supposed to be an analogue of (part of) the world being modeled. FOL

very simple kind of model, in which objects in the world (not necessarily phyobjects) are modeled as elements of a set, and relationships between ob

modeled as sets of tuples.



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This is exactly the same kind of model asused in a database: objects in the worldare modeled as values (elements) andrelationships as tables (sets of tuples).
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Documents

0 an Introduction to SNOMED CT1