Slide No.: 1 OpenGALEN Introduction to Clinical Introduction to Clinical Terminology and Terminology and Classification Classification Clinical Decision Support Clinical Decision Support L4 L4 AL Rector OpenGALEN TopThing UK The Medical Informatics Group, U of Manchester www.cs.man.ac.uk/mig/galen www.opengalen.org www.topthing.com [email protected]
46
Embed
OpenGALEN Slide No.: 1 Introduction to Clinical Terminology and Classification Clinical Decision Support L4 AL Rector OpenGALEN TopThing UK The Medical.
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Slide No.: 1 OpenGALEN
Introduction to Clinical Terminology Introduction to Clinical Terminology and Classification and Classification
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 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
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
Slide No.: 6 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.: 7 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
— 10 x larger than ICD; aimed at US insurance reimbursement10 x larger than ICD; aimed at US insurance reimbursement
Slide No.: 8 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
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
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.: 11 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.: 12 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
Enumerated Systems Enumerated Systems in coping with these changesin coping with these changes
Slide No.: 14 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.: 15 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.: 16 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.: 17 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.: 18 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......
Easy to process but... Reorganisation requires changing codesReorganisation requires changing codes Codes cannot be permanentCodes cannot be permanent
Slide No.: 19 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.: 20 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.: 21 OpenGALEN
Problem (7): Language is Problem (7): Language is slippery:slippery:
Two hands or Four?Two hands or Four?
Slide No.: 22 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.: 23 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.: 24 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.: 25 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
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
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.: 31 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
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
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
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.: 34 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
SNOMED-RT (SNOMED-CT?)— 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)
GALEN derived terminologies UK Drug OntologyUK Drug Ontology Procedure classificationsProcedure classifications
Slide No.: 36 OpenGALEN
Generation 2.5 Pre-coordinatedGeneration 2.5 Pre-coordinatedFormal Compositions More Formal Compositions More
semanticssemantics Limited ability to cope with combinatorial explosion
Any one pre-coordinated terminology of fixed sizeAny one pre-coordinated terminology of fixed size— but arbitrarily many terminologies might be derivedbut arbitrarily many terminologies might be derived
Limited ability to cope with fractal knowledge Limited extensibilityLimited extensibility
— Extensibility requires access to ‘Workbench’Extensibility requires access to ‘Workbench’— Bottom up / middle outBottom up / middle out
More explicit information Logical criteria for correctness / redundancy / equivalenceLogical criteria for correctness / redundancy / equivalence
— Based on knowledge representation (ontologies) and description logicsBased on knowledge representation (ontologies) and description logics
Limited support for data capture and user interface
Indefinitely many compositions possibleIndefinitely many compositions possible— Lists not pre-enumeratedLists not pre-enumerated
Copes with fractal knowledgeCopes with fractal knowledge— Easily extensible to add more detailEasily extensible to add more detail
Most information explicit More comprehensive ontology (50-250 links)More comprehensive ontology (50-250 links)
Good support for data capture / user interface But requires additional pragmatic knowledge layerBut requires additional pragmatic knowledge layer
Separates user view and machine view Intermediate representation vs GRAILIntermediate representation vs GRAIL
Slide No.: 39 OpenGALEN
Case Study 1: Case Study 1: The exploding bicycleThe exploding bicycle
ICD-9 (E826) 8
READ-2 (T30..) 81
READ-3 87
ICD-10 (V10-19) 587 V31.22 Occupant of three-wheeled motor vehicle injured in collision with pedal cycle, person
on outside of vehicle, nontraffic accident, while working for income
W65.40 Drowning and submersion while in bath-tub, street and highway, while engaged in sports activity
X35.44 Victim of volcanic eruption, street and highway, while resting, sleeping, eating or engaging in other vital activities
Slide No.: 41 OpenGALEN
Defusing the exploding bicycle:Defusing the exploding bicycle:500 codes in pieces500 codes in pieces
10 things to hit… Pedestrian / cycle / motorbike / car / HGV / train / unpowered Pedestrian / cycle / motorbike / car / HGV / train / unpowered
vehicle / a tree / othervehicle / a tree / other
5 roles for the injured… Driving / passenger / cyclist / getting in / otherDriving / passenger / cyclist / getting in / other
5 activities when injured… resting / at work / sporting / at leisure / otherresting / at work / sporting / at leisure / other
2 contexts… In traffic / not in trafficIn traffic / not in traffic
V12.24 Pedal cyclist injured in collision with two- or three-wheeled motor vehicle, unspecified pedal cyclist, nontraffic accident, while resting, sleeping, eating or engaging in other vital activities
Slide No.: 42 OpenGALEN
Goodbye to picking lists…Goodbye to picking lists… Structured Data Entry
File Edit Help
What you hit
Your Role
Activity
Location
Cycling Accident Cycling Accident
Slide No.: 43 OpenGALEN
Other important links and Other important links and initiativesinitiatives
HL7 Vocabulary group See HL7 web siteSee HL7 web site
— Or join list serverOr join list server
SNOMED-DICOM-Microglossary (Radiology)
Nursing initiatives - see Nick Hardiker papers
ISO TC215 WG2 / CEN TC251 WG3 See web sitesSee web sites
Slide No.: 44 OpenGALE
N
Criteria for successCriteria for success
Re-use A recognised growing library of common decsision support A recognised growing library of common decsision support
modulesmodules— Stop starting from scratch!Stop starting from scratch!
Integration 2+ independently developed DSSs 2+ independently developed DSSs integrated withintegrated with
2+ independently developed EPRS 2+ independently developed EPRS withoutwithoutexponentially increasing effort. exponentially increasing effort.
Slide No.: 45 OpenGALE
N
Criteria for successCriteria for success
Authoring No individual invests in their own terminologyNo individual invests in their own terminology
Indexing Simplification of systems Simplification of systems
— a sharp drop in special cases and exceptionsa sharp drop in special cases and exceptions— a sharp increase in authors’ productivitya sharp increase in authors’ productivity
Slide No.: 46 OpenGALE
N
Criteria for successCriteria for success
User interfaces Real systems in real use with real patients by real cliniciansReal systems in real use with real patients by real clinicians