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Introduction to Clinical Terminology and Classification. AL Rector Open GALEN CO-ODE The Medical Informatics Group, U of Manchester www.cs.man.ac.uk/mig/galen www.opengalen.org www.co-ode.org oiled.man.ac.uk [email protected]. Clinical Terminology. Data Entry. Clinical Record. - PowerPoint PPT Presentation
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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
Slide No.: 2 OpenGALEN
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
Slide No.: 3 OpenGALEN
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?”
Slide No.: 4 OpenGALEN
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
Slide No.: 5 OpenGALEN
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
Slide No.: 6 OpenGALEN
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
Slide No.: 7 OpenGALEN
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)
Slide No.: 8 OpenGALEN
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
Slide No.: 9 OpenGALEN
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
Slide No.: 10 OpenGALEN
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
Slide No.: 11 OpenGALEN
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— ……
Slide No.: 12 OpenGALEN
History (3)History (3)
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
Slide No.: 13 OpenGALEN
History (4)History (4)
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
Slide No.: 14 OpenGALEN
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
Slide No.: 15 OpenGALEN
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
Slide No.: 16 OpenGALEN
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
Slide No.: 17 OpenGALEN
Problems withProblems with‘First Generation’‘First Generation’
Enumerated Systems Enumerated Systems in coping with these changesin coping with these changes
Slide No.: 18 OpenGALEN
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
Slide No.: 19 OpenGALEN
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
Slide No.: 20 OpenGALEN
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
Slide No.: 21 OpenGALEN
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
Slide No.: 22 OpenGALEN
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
Slide No.: 23 OpenGALEN
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
Slide No.: 24 OpenGALEN
Problems (5)Problems (5)
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!
Slide No.: 25 OpenGALEN
Problems (6)Problems (6)
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
Slide No.: 26 OpenGALEN
Problem (7): Language is Problem (7): Language is slippery:slippery:
Two hands or Four?Two hands or Four?
Slide No.: 27 OpenGALEN
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
Slide No.: 28 OpenGALEN
Problems (8)Problems (8)
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, ...
Slide No.: 29 OpenGALEN
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
Slide No.: 30 OpenGALEN
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
Slide No.: 31 OpenGALEN
Cimino’s Desiderata (2)Cimino’s Desiderata (2)
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
Slide No.: 32 OpenGALEN
Cimino’s Desiderata (3)Cimino’s Desiderata (3)
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?
Slide No.: 33 OpenGALEN
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
Slide No.: 35 OpenGALEN
Cross mapped and typed Cross mapped and typed terminologies & terminologies &
vocabulariesvocabularies
Slide No.: 36 OpenGALEN
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.
Slide No.: 37 OpenGALEN
Slide No.: 38 OpenGALEN
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
Slide No.: 39 OpenGALEN
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
Slide No.: 40 OpenGALEN
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
Slide No.: 41 OpenGALEN
Slide No.: 42 OpenGALEN
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
Slide No.: 43 OpenGALEN
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
Slide No.: 44 OpenGALEN
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
Slide No.: 45 OpenGALEN
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
Slide No.: 46 OpenGALEN
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
Slide No.: 47 OpenGALEN
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
Slide No.: 48 OpenGALEN
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
Slide No.: 49 OpenGALEN
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
Slide No.: 50 OpenGALEN
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
Slide No.: 51 OpenGALEN
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
Slide No.: 52 OpenGALEN
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
Slide No.: 53 OpenGALEN
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”
Slide No.: 54 OpenGALEN
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