OpenGALEN Slide No.: 1 Introduction to Clinical Terminology and Classification AL Rector OpenGALEN...

Slide No.: 1 OpenGALEN

Introduction to Clinical Terminology Introduction to Clinical Terminology and Classification and Classification

AL Rector OpenGALEN

CO-ODEThe Medical Informatics Group, U of Manchester

www.cs.man.ac.uk/mig/galenwww.opengalen.org

www.co-ode.orgoiled.man.ac.uk

[email protected]


Where we come fromWhere we come from

Best Practice

Clinical Terminology

Data Entry

Clinical Record

Decision Support

Best Practice

Data Entry

Electronic Health

Records

Decision Support &Aggregated

Data

GALEN Clinical Terminology


OpenOpenGALEN: GALEN: PhilosophyPhilosophy

Terminology is software Terminology is the interface between people and machinesTerminology is the interface between people and machines

Re-use is the key Patient-centred informationPatient-centred information

Terminology must have a purpose Always ask: Always ask: “What’s it for?”“What’s it for?”

— Not art for art’s sakeNot art for art’s sake Terminology supports clinical applications - not vice versaTerminology supports clinical applications - not vice versa

– Applications for someone to do something for somebodyApplications for someone to do something for somebody– Keep the ‘Horse before the Cart’Keep the ‘Horse before the Cart’

Always ask: Always ask: “How will we know if it works?”“How will we know if it works?” “How will we know if it fails?” “How will we know if it fails?”


OpenOpenGALEN: GALEN: Key ideasKey ideas

Separation of kinds of knowledge Terminology, medical record and information system schemasTerminology, medical record and information system schemas Models of meaning; Models of UseModels of meaning; Models of Use Concepts, language, Coding, Indexing, PragmaticsConcepts, language, Coding, Indexing, Pragmatics Machine level, User level Machine level, User level

Knowledge is fractal! There will always be more detail to be addedThere will always be more detail to be added

— Therefore terminologies must be extensibleTherefore terminologies must be extensible

Formal logical Support Too big and complicated to maintain by handToo big and complicated to maintain by hand

— Extensibility requires rulesExtensibility requires rules— Software needs logical rigourSoftware needs logical rigour


Axes for kinds of KnowledgeAxes for kinds of Knowledge

Machine level

Human Level

Concepts

Language

Coding

Indexing

Pragmatics & User Interface

Terminology

Medical Records/Information systems

Decision Support rules


9) Interface of EHR, Messaging 9) Interface of EHR, Messaging & Decision Support& Decision Support

interfaceinterface

interface

Concept Model(Ontology)

Information Model(Patient Data Model)

Inference Model(Guideline Model)

Dynamic Guideline Knowledge

Static Domain Knowledge

Patient Specific Records

Significant Research Topic Now


Uses of TerminologyUses of Terminology

Clinical Epidemiology and quality assuranceEpidemiology and quality assurance Reproducibility / ComparabilityReproducibility / Comparability IndexingIndexing

Software Re-useRe-use ! ! Integration and Messaging between systemsIntegration and Messaging between systems Authoring and configuring systemsAuthoring and configuring systems Data capture and presentation (user interface)Data capture and presentation (user interface) Indexing information and knowledge (meta-data, The Web)Indexing information and knowledge (meta-data, The Web)


An Old ProblemAn Old Problem“On those remote pages it is written that animals are divided

into:

a. those that belong to the Emperor b. embalmed ones c. those that are trained d. suckling pigse. mermaids f. fabulous ones g. stray dogs h. those that are included in this classificationi. those that tremble as if they were mad j. innumerable ones k. those drawn with a very fine camel's hair brush l. others m. those that have just broken a flower vase n. those that resemble flies from a distance"

From The Celestial Emporium of Benevolent Knowledge, Borges


History:History:Origins of existing Origins of existing

terminologiesterminologies Epidemiology

ICD - Farr in 1860s to ICD9 in 1979ICD - Farr in 1860s to ICD9 in 1979— International reporting of morbidity/mortalityInternational reporting of morbidity/mortality

ICPC - 1980sICPC - 1980s— Clinically validated epidemiology in primary careClinically validated epidemiology in primary care

Now expanded for use in Dutch GP softwareNow expanded for use in Dutch GP software

Librarianship MeSH - NLM from around 1900 - Index Medicus & MedlineMeSH - NLM from around 1900 - Index Medicus & Medline EMTree - from Elsevier in 1950s - EMBase EMTree - from Elsevier in 1950s - EMBase

Remumeration ICD9-CM (Clinical Modification) 1980ICD9-CM (Clinical Modification) 1980

— 10 x larger than ICD; aimed at US insurance reimbursement10 x larger than ICD; aimed at US insurance reimbursement


Traditional SystemsTraditional Systems Built by people for interpretation by people (Coding clerks)

Most knowledge Most knowledge implicit implicit in rubricsin rubrics— Must understand medicine to use intelligentlyMust understand medicine to use intelligently Not built for softwareNot built for software

On paper for use on paper EnumeratedEnumerated - top down all possibilities listed - top down all possibilities listed

— Serial - Single use - Single ViewSerial - Single use - Single View

Hierarchical Thesauri Traditional terminological techniques from librarianshipTraditional terminological techniques from librarianship

— ‘‘Broader than’ / ‘Narrower than’ (ISO 1087)Broader than’ / ‘Narrower than’ (ISO 1087) no logical foundationno logical foundation

Focused on ‘terms’ Language and concepts mixedLanguage and concepts mixed

— Synonyms, preferred terms, etc caused confusionSynonyms, preferred terms, etc caused confusion


History (2)History (2)

Pathology indexing SNOMED 1970s to 1990 (SNOMED International)SNOMED 1970s to 1990 (SNOMED International)

— First faceted or combinatorial systemFirst faceted or combinatorial system Topology, morphology, aetiology, functionTopology, morphology, aetiology, function Plus diseases cross referenced to ICD9Plus diseases cross referenced to ICD9

Specialty Systems Mostly similar hierarchical systemsMostly similar hierarchical systems

— ACRNEMA/SDM - RadiologyACRNEMA/SDM - Radiology— NANDA, ICNP… - NursingNANDA, ICNP… - Nursing— ……



Early computer systems Read I (4 digit Read)Read I (4 digit Read)

— Aimed at saving space on early computersAimed at saving space on early computers 1-5 Mbyte / 10,000 patients1-5 Mbyte / 10,000 patients

— Hierarchical modelled on ICD9Hierarchical modelled on ICD9 Detailed signs and symptoms for primary careDetailed signs and symptoms for primary care Purchased by UK government in 1990Purchased by UK government in 1990

— Single useSingle use Morbidity indexingMorbidity indexing

Medical Entities Dictionary (MED) Medical Entities Dictionary (MED) — Jim CiminoJim Cimino



Aspirations for electronic patient records (EPRs) Weed’s Problem Oriented Medical RecordWeed’s Problem Oriented Medical Record

— Direct entry by health care professionalsDirect entry by health care professionals

Aspirations for decision support Ted Shortliffe (MYCIN), Clem McDonald (Computer based Ted Shortliffe (MYCIN), Clem McDonald (Computer based

reminders), Perry Miller (Critiquing),..reminders), Perry Miller (Critiquing),..

Aspirations for re-use Patient centred informationPatient centred information

Needed common multi-use multi-purpose terminology None workedNone worked


Motivations and Business Motivations and Business ModelsModels

Remuneration ICD9/10-CM in US for insurance and medicare for diseasesICD9/10-CM in US for insurance and medicare for diseases Clinical Procedures Terminology (CPT) for surgical proceduresClinical Procedures Terminology (CPT) for surgical procedures

Public Health Reporting ICD9/10ICD9/10

Clinical Recording Read 1-3, SNOMED-RT/CTRead 1-3, SNOMED-RT/CT ICPC – International Classification of Diseases in Primary CareICPC – International Classification of Diseases in Primary Care

Indexing publications MeSH – Medical Subject Headings - Basis of indexing MedLine/PubMedMeSH – Medical Subject Headings - Basis of indexing MedLine/PubMed EMTree – basis of indexing EMBASEEMTree – basis of indexing EMBASE

Support for applications and decision support GALENGALEN


Summary of Changes at end of Summary of Changes at end of 1st Generation1st Generation

From terminologies for people to terminologies for machines

From paper to software

From single use to multiple re-use for patient centred systems

From entry by coding clerks to direct entry by health care professionals

From pre-defined reporting for statistics to reliable indexing for decision support


Changes at end of first Changes at end of first generationgeneration

From models of USE to models of MEANING But tended to lose the model of useBut tended to lose the model of use

— The goal of “useful and usable systems” lostThe goal of “useful and usable systems” lost


Problems withProblems with‘First Generation’‘First Generation’

Enumerated Systems Enumerated Systems in coping with these changesin coping with these changes


Problems (1)Problems (1) Scaling !!!

More detail and more specialities required scaling up, but...More detail and more specialities required scaling up, but...

The combinatorial explosion Example: Burns:Example: Burns:

— 100 sites x 3 depths 100 sites x 3 depths 404 codes 404 codes 5 subsites/site x chemical or thermal 5 subsites/site x chemical or thermal 7272 7272

– x 3 extents x 3 durations x 3 extents x 3 durations 116,352

‘‘The Persian chessboard’The Persian chessboard’— 2264 64 1019

1019 grains of rice 100 billion tonnes of rice 1019 nanoseconds 10,000 years

Read II grew from 20,000 to 250,000 terms in ~100 staff-years Read II grew from 20,000 to 250,000 terms in ~100 staff-years — still too small to be usefulstill too small to be useful

but too big to use but too big to use


BenefitsBenefits Avoid the “Exploding Bicycle”

From “phrase book” to “dictionary + grammar” Tame combinatorial explosions

1980 - ICD-9 (E826) 8 1980 - ICD-9 (E826) 8 1990 - READ-2 (T30..) 811990 - READ-2 (T30..) 81 1995 - READ-3 871995 - READ-3 87 1996 - ICD-10 (V10-19) 5871996 - ICD-10 (V10-19) 587

— V31.22 Occupant of three-wheeled motor vehicle injured in collision with pedal V31.22 Occupant of three-wheeled motor vehicle injured in collision with pedal cycle, person on outside of vehicle, nontraffic accident, while working for cycle, person on outside of vehicle, nontraffic accident, while working for incomeincome

and meanwhile elsewhere in ICD-10and meanwhile elsewhere in ICD-10— W65.40 Drowning and submersion while in bath-tub, street and highway, while W65.40 Drowning and submersion while in bath-tub, street and highway, while

engaged in sports activityengaged in sports activity

— X35.44 Victim of volcanic eruption, street and highway, while resting, sleeping, X35.44 Victim of volcanic eruption, street and highway, while resting, sleeping, eating or engaging in other vital activitieseating or engaging in other vital activities


Problems (2)Problems (2)

Information implicit in the rubrics ““Hypertension excluding pregancy”Hypertension excluding pregancy”

— Computers can’t read!Computers can’t read! Invisible to softwareInvisible to software

No explicit information except the hierarchyNo explicit information except the hierarchy— Minimal support for softwareMinimal support for software— No opportunity to use softwre to helpNo opportunity to use softwre to help

Language and concepts confused SynonymsSynonyms Preferred termsPreferred terms HomonymsHomonyms Only simple look up and spelling correctionOnly simple look up and spelling correction


Problems (3)Problems (3) Mixed Organisation

‘‘Heart diseases’ in 13 of 19 chapters of ICDHeart diseases’ in 13 of 19 chapters of ICD— Tumours, infections, congenital abnormalities, toxic, …Tumours, infections, congenital abnormalities, toxic, …

‘‘Steroids’ in five chapters of standard drug classificationsSteroids’ in five chapters of standard drug classifications— Anti-inflammatories, anthi-asthmatics, …Anti-inflammatories, anthi-asthmatics, …

Unreliable for indexing or AbstractionsUnreliable for indexing or Abstractions— How to say something about ‘all heart diseases’?How to say something about ‘all heart diseases’?

Fixed organisation Single hierarchy - Single useSingle hierarchy - Single use

— Where to put ‘gout’ - arthritis or metabolic disease?Where to put ‘gout’ - arthritis or metabolic disease? Back and forth in each edition of ICDBack and forth in each edition of ICD

— No re-useNo re-use


Problems 3bProblems 3bThesauri rather than Thesauri rather than

ClassificationsClassificationsorgan } kind heart } part heart valve } kind aortic valve } part aortic valve cusp

A Mixed Hierarchy

disorder of organ

disorder of heart

disorder of valve in heart

disorder of aortic valve in heart

disorder of cusp in aortic valve in heart

A correct kind-of (subsumption) hierarchy


Problems (4)Problems (4) ‘Semantic identifiers’

Codes really paths - moving a concept meant changing its codeCodes really paths - moving a concept meant changing its code

3 Cardiovascular disorders……3.4 Disorders of Artery3.4 Disorders of Artery......

......3.4.2 Disorders of coronary artery3.4.2 Disorders of coronary artery......

……3.4.2.3 Coronary thrombosis3.4.2.3 Coronary thrombosis……

Easy to process but... Reorganisation requires changing codesReorganisation requires changing codes Codes cannot be permanentCodes cannot be permanent



Maintenance 20 Years from ICD9 to ICD1020 Years from ICD9 to ICD10 ~100 person-years from Read 1 to Read 3~100 person-years from Read 1 to Read 3 Mega francs/guilders/crowns/marks on European coding schemesMega francs/guilders/crowns/marks on European coding schemes Thousands of unpaid hours of committee timeThousands of unpaid hours of committee time

— Impossible / meaningless decisions take longestImpossible / meaningless decisions take longest You can search forever for something that is not thereYou can search forever for something that is not there

— Multiple uses compete - Multiple uses compete - Must choose one useMust choose one use

– Most successful were clear about their purpose - ICD, ICPC, MeSHMost successful were clear about their purpose - ICD, ICPC, MeSH

Codes change meaning with version changes Old data misleading!Old data misleading!



Version specific artefacts ““Not otherwise specified” (NOS)Not otherwise specified” (NOS)

— Used to move a general concept ‘down’Used to move a general concept ‘down’ Not elsewhere classified (NEC)Not elsewhere classified (NEC)

— Catch all - Nowhere else in coding system e.g. ‘Tumour not Catch all - Nowhere else in coding system e.g. ‘Tumour not elsewhere classified’ elsewhere classified’

dependent on version, dependent on version,

““Other”Other”— Catch all - Not listed below, e.g. “Other diseases of the Catch all - Not listed below, e.g. “Other diseases of the

cardiovascular system”cardiovascular system” dependent on versiondependent on version

Not used consistsently


Problem (7): Language is Problem (7): Language is slippery:slippery:

Two hands or Four?Two hands or Four?


Language/Concepts are Language/Concepts are slipperyslippery

Human cognition makes it look easy Logic fails to capture itLogic fails to capture it

— Classification is easy until you try to do itClassification is easy until you try to do it Trying since Aristotle in the West and Ancient Chinese in the EastTrying since Aristotle in the West and Ancient Chinese in the East

Words/Concepts mean what a community decides they mean Does a chimpanzee have four hands?Does a chimpanzee have four hands? Is a prion alive?Is a prion alive? Is surgery on the ovary a kind of ‘Endocrine surgery’?Is surgery on the ovary a kind of ‘Endocrine surgery’?

Easier to agree on the concrete than the abstract Easy to agree on useful abstractions and generalisationsEasy to agree on useful abstractions and generalisations

— Harder to agree on how to name themHarder to agree on how to name them



There is no re-use - there is no standard The ‘grand challenge’: A common controlled vocabulary for medicineThe ‘grand challenge’: A common controlled vocabulary for medicine

— But But re-usere-use requires multiple different views requires multiple different views People’s needs differ / People do and find different thingsPeople’s needs differ / People do and find different things

— By professionBy profession Doctors and specialties, nurses, physiotherapiests, dentists…Doctors and specialties, nurses, physiotherapiests, dentists…

— By situationBy situation Inpatient, outpatient, primary care, community…Inpatient, outpatient, primary care, community…

— By taskBy task Diagnosis, management, prescribing, Diagnosis, management, prescribing, patient care, public health, quality assurance, management, planningpatient care, public health, quality assurance, management, planning

— By country and communityBy country and community US, UK, France, Germany, Japan, Korea, ... US, UK, France, Germany, Japan, Korea, ...


Summary of ProblemsSummary of Problems1st Generation Enumerated 1st Generation Enumerated

SystemsSystems Enumerated Single Hierarchies

List all possibilities in advanceList all possibilities in advance— Cannot cope with fractal knowledgeCannot cope with fractal knowledge

Most knowledge implicitMost knowledge implicit— Invisible to softwareInvisible to software

Can’t agree on common concepts and classificationCan’t agree on common concepts and classification— Unreliable for indexingUnreliable for indexing

Difficult to use for healthcare professionals No support for user interfaceNo support for user interface

Can’t build and maintain big classifications Language and concepts don’t translate easily to logic and softwareLanguage and concepts don’t translate easily to logic and software


Cimino’s Desiderata (1)Cimino’s Desiderata (1)

Concept orientation Separate language (terms) and concepts (codes)Separate language (terms) and concepts (codes)

Concept permanence Never re-use a code (‘retire’ it)Never re-use a code (‘retire’ it)

Nonsemantic concept identifiers Separate the code from the pathSeparate the code from the path

Polyhierarchy Allow one concept to be classified in multiple waysAllow one concept to be classified in multiple ways

— Gout can be Gout can be bothboth a metabolic disease and an arthritis a metabolic disease and an arthritis



Formal Definitions i.e ‘Be compositional’i.e ‘Be compositional’

Reject ‘Not elsewhere classified’ concept permanence and NECconcept permanence and NEC

Multiple granularities Organ, tissue, cellular, molecularOrgan, tissue, cellular, molecular Grades, types, classes of diseasesGrades, types, classes of diseases Special clinical criteriaSpecial clinical criteria

Multiple consistsent views Allow different organisationsAllow different organisations

— e.g. functional, anatomical, pathologicale.g. functional, anatomical, pathological



Represent context Family history, risk, source of informationFamily history, risk, source of information

Evolve gracefully Allow controlled changesAllow controlled changes

Recognise redundancy (equivalence) ‘‘Carcinoma’ + ‘Lung’ ?=? ‘Carcinoma of the lung’Carcinoma’ + ‘Lung’ ?=? ‘Carcinoma of the lung’

— How would we know?How would we know? How could How could a machinea machine know? know?


Solution 0: You are worrying Solution 0: You are worrying about the wrong problemabout the wrong problem

International Classification of Primary Care (ICPC) Focus on repeatability and quality across languages for a Focus on repeatability and quality across languages for a

small (<2000) number of codessmall (<2000) number of codes

OpenGALEN

Solution Generation 1Solution Generation 1Megaterm + Crossmapping = UMLSMegaterm + Crossmapping = UMLS

Clinical Applications

Medical Records

Data entry

Decision support

UMLS

Medical Records

Data entry

Decision support

MEGA-TERM

Coding &Classification

ICD-9 ICD-10

MeSHACRNEMA

ICPC

SNOMED Axes

READ

OPCS


Cross mapped and typed Cross mapped and typed terminologies & terminologies &

vocabulariesvocabularies


The UMLS Knowledge SourcesThe UMLS Knowledge Sources

Metathesaurus Cross mappingsCross mappings

Language resources NORM – stemming and term recognitionNORM – stemming and term recognition

UMLS Semantic Net 170 types attached to categorise concepts170 types attached to categorise concepts

— Disease, anatomical part, micro-organism, etc.Disease, anatomical part, micro-organism, etc.


Unified Medical Language System (UMLS) from US National Library of Medicine

Defacto common registry for vocabulariesDefacto common registry for vocabularies— Concept Unique Identifiers (CUIs) and Lexical Unique Identifiers Concept Unique Identifiers (CUIs) and Lexical Unique Identifiers

(LUIs) are defacto the common nomenclature (LUIs) are defacto the common nomenclature NB must use a CUI + LUI to get unique identificationNB must use a CUI + LUI to get unique identification

Licence termsLicence terms— Class I – free for useClass I – free for use— Clsass III – heavily restrictedClsass III – heavily restricted— (Class II – almost nonexistent)(Class II – almost nonexistent)

Solution 1 Cross-mapping & Solution 1 Cross-mapping & UMLS UMLS


Solution 1 Cross-mapping & Solution 1 Cross-mapping & UMLS UMLS

An invaluable resource, but... No better than the vocabularies which are mappedNo better than the vocabularies which are mapped

— Limited detail for patient careLimited detail for patient care— Unreliable for indexing or abstraction of knowledgeUnreliable for indexing or abstraction of knowledge— Best for relating everything to MeSH for indexing literatureBest for relating everything to MeSH for indexing literature

Still limited by combinatorial explosionStill limited by combinatorial explosion— Still can’t cope with fractal knowledgeStill can’t cope with fractal knowledge

Not extensible - no help in building or extending terminologieseNot extensible - no help in building or extending terminologiese No help in reorganising existing terminologies to re-use for new No help in reorganising existing terminologies to re-use for new

purposespurposes Top downTop down

Information still implicitInformation still implicit— Minimal help with softwareMinimal help with software

No help with data capture, user interfacesNo help with data capture, user interfaces


Solution IIa: Build what you Solution IIa: Build what you need as you need itneed as you need it

LOINC – dominant coding system for laboratory systems(“Logical Observation Identifiers Names and Codes”)http://www.loinc.org/

Clinical LOINC contains increasing amounts of clinical references

Fully Class I included in UMLSFully Class I included in UMLS

Closely linked to HL7 and HL7 vocabulary committee


Build and Control what you Build and Control what you need onlyneed only

HL7 Messaging standard Controls the codes that hold messages together Controls the codes that hold messages together Uses codes from elsewhere as ‘payload’Uses codes from elsewhere as ‘payload’ See See www.hl7.orgwww.hl7.org

— (Possib ly the world’s worst web site)(Possib ly the world’s worst web site)— Some material members onlySome material members only


Solutions Generations 2-3Solutions Generations 2-3Compositional SystemsCompositional Systems

Beat the combinatorial explosion Build concepts out of pieces - leggo Build concepts out of pieces - leggo

— Dictionary and grammar rather than phrasebookDictionary and grammar rather than phrasebook But hardBut hard


Solution Generation 1.5: FacetedSolution Generation 1.5: Faceted Faceted systems: SNOMED International

— Inflammation + Lung + Infection + Pneumococcus Inflammation + Lung + Infection + Pneumococcus Pneumoccal pneumonia Pneumoccal pneumonia

Limit combinatorial explosion, but… Rigid - a limited number of axes / facets / chaptersRigid - a limited number of axes / facets / chapters Each facet has the problems of a first generation enumerated systemEach facet has the problems of a first generation enumerated system

— Much knowledge still implicitMuch knowledge still implicit No way to know how identifiers relateNo way to know how identifiers relate

— No explicit relations, only ‘+’No explicit relations, only ‘+’— No way to recognise redundancy / equivalenceNo way to recognise redundancy / equivalence— No help with data capture or user interface / No way to recognise nonsenseNo help with data capture or user interface / No way to recognise nonsense

Carcinoma + Hair + Donkey + Emotional Carcinoma + Hair + Donkey + Emotional ???? ????

Still can’t cope with fractal knowledgeStill can’t cope with fractal knowledge— Limited extensibility: limited help with building, extending or reorganisingLimited extensibility: limited help with building, extending or reorganising

Still Top DownStill Top Down


Generation 2: Enumerated Generation 2: Enumerated CompositionalCompositional

Read III with qualifiers— Inflammation: site: lung, cause: pneumococcus Inflammation: site: lung, cause: pneumococcus Pnemococcal Pneumonia Pnemococcal Pneumonia

More semantics but… Limited qualifiers - limited views - limited re-useLimited qualifiers - limited views - limited re-use Limited help with data capture - User interface difficultLimited help with data capture - User interface difficult Much information still implicit - limited software supportMuch information still implicit - limited software support

— No way to recognise redundancy / equivalence / errorsNo way to recognise redundancy / equivalence / errors— Organisation still mixed - indexing better but still unreliableOrganisation still mixed - indexing better but still unreliable

Limited separation of language and concepts Limited separation of language and concepts Still can’t cope with fractal knowledgeStill can’t cope with fractal knowledge

— Limited extensibility; limited help with building and reorganising terminologiesLimited extensibility; limited help with building and reorganising terminologies Top down Top down


Encrustation

+ involves: MitralValve

Thing

+ feature: pathological

Structure

+ feature: pathological

+ involves: Heart

Logic Based Ontologies: The basicsLogic Based Ontologies: The basics

Thing

Structure

Heart MitralValve EncrustationMitralValve* ALWAYS partOf: Heart

Encrustation* ALWAYS feature: pathological

Feature

pathological red

+ (feature: pathological)

red

+ partOf: Heart

red

+ partOf: Heart

Primitive skeleton Descriptions Definitions Reasoning Validating


CT VocabularyCT Vocabulary

“Reference Terminology” vs “Interface Terminologies” Reference terminology = enumerated hierarchy of formally Reference terminology = enumerated hierarchy of formally

defined termsdefined terms Interface terminology = navigation structure for user interfaceInterface terminology = navigation structure for user interface

— Explicitly excluded from SNOMED-RTExplicitly excluded from SNOMED-RT

“Terming”, “Coding”, and “Grouping” Terming - finding the lexical stringTerming - finding the lexical string Coding - finding the correct unique code (concept)Coding - finding the correct unique code (concept) Grouping - putting codes into groupers for epidmiological or Grouping - putting codes into groupers for epidmiological or

other purposesother purposes


Generation 2.5 Pre-coordinatedGeneration 2.5 Pre-coordinatedFormal CompositionsFormal Compositions

SNOMED-CT Formal collaboration between College of American Formal collaboration between College of American

Pathologists (CAP/SNOMED) and NHSPathologists (CAP/SNOMED) and NHS— Formal logical model for classifying a fixed list of definitionsFormal logical model for classifying a fixed list of definitions— Simple fixed ontology (7 links)Simple fixed ontology (7 links)

Now officially adopted and Now officially adopted and probablyprobably available for both NHS available for both NHS and related academic usesand related academic uses

GALEN derived terminologies UK Drug OntologyUK Drug Ontology Procedure classificationsProcedure classifications


Generation IIIGeneration III

Fully compositional post coordinated Not yet in use or fully availableNot yet in use or fully available

— GALEN-likeGALEN-like Will probably arrive with Semantic WebWill probably arrive with Semantic Web


Other Key ResourcesOther Key Resources Anatomy

Digital Anatomist Foundational Model of AnatomyDigital Anatomist Foundational Model of Anatomy— University of Washington (http://sig.biostr.washington.edu/projects/da/)University of Washington (http://sig.biostr.washington.edu/projects/da/)

Comprehensive model of STRUCTURAL anatomyComprehensive model of STRUCTURAL anatomy Transformed into formal representation in Freiburg Transformed into formal representation in Freiburg

– Feasibility rather than productionFeasibility rather than production MouseMouse

— The Edinburgh Mouse Atlas Project (http://genex.hgu.mrc.ac.uk/)The Edinburgh Mouse Atlas Project (http://genex.hgu.mrc.ac.uk/)

Bioinformatics GO - The Gene OntologyGO - The Gene Ontology MGED – Mircroarray Gene Expression Data MGED – Mircroarray Gene Expression Data OMIM – Online Mendelian Inheritance in ManOMIM – Online Mendelian Inheritance in Man

Drugs Proprietary databases – First Databank, MicromedProprietary databases – First Databank, Micromed UK Drug Dictionary (UKCPRS)UK Drug Dictionary (UKCPRS)

National Cancer Institute CaCore Ontologies


Current Status (1)Current Status (1) UMLS is the central coordinating force

Any terminology needs links links to CUIs and LUIsAny terminology needs links links to CUIs and LUIs— Many people using CLASS I licensed terms onlyMany people using CLASS I licensed terms only

Links to MeSH and PubMedLinks to MeSH and PubMed

ICD9/10-CM used for reporting of diseases for insurance and Medicare in the US

ICD-10 used for official reporting in UKICD-10 used for official reporting in UK

CPT and OPCS used for reporting of procedures in US and UK respectively

SNOMED-CT purchased by US and mandated in UK As yet few convincing As yet few convincing


Current Status (2)Current Status (2)

ICPC widely used in in primary care on continent, especially in the Netherlands

LOINC used for lab systems; HL7 for messaging

Variants of SNOMED used for pathology many places

Many specialist systems SNOMED-DICOM-Microglossary (SDM) for imagingSNOMED-DICOM-Microglossary (SDM) for imaging

— Unrelated to SNOMEDUnrelated to SNOMED Several nursing systemsSeveral nursing systems

A variety of open source resources appearing


Current Status (3)Current Status (3)

Commercial world dominated by proprietary systems MedCinMedCin All based on “Model of Use”All based on “Model of Use”


The Semantic Web and OWLThe Semantic Web and OWL

“Ontologies” – fancy word for terminologies Means many things to many peopleMeans many things to many people

W3C has produced a standard language for compositional “logic based” ontologies, OWL

““OIL” + “DAML” OIL” + “DAML” “DAML+OIL” “DAML+OIL” “OWL” “OWL”— See oiled.man.ac.ukSee oiled.man.ac.uk— See www.co-ode.orgSee www.co-ode.org— See http://www.w3.org/2001/sw/WebOnt/See http://www.w3.org/2001/sw/WebOnt/

Rapid proliferation of open source tools and resources No longer a biomedical problem onlyNo longer a biomedical problem only Serious computer scientists finally involvedSerious computer scientists finally involved

OpenGALEN Slide No.: 1 Introduction to Clinical Terminology and Classification AL Rector OpenGALEN...

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