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MIE06 TUTORIAL USE1 An Ontology driven collaborative development for biomedical terminologies: from the French CCAM to the Australian ICHI coding system.

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Presentation on theme: "MIE06 TUTORIAL USE1 An Ontology driven collaborative development for biomedical terminologies: from the French CCAM to the Australian ICHI coding system."— Presentation transcript:

1 MIE06 TUTORIAL USE1 An Ontology driven collaborative development for biomedical terminologies: from the French CCAM to the Australian ICHI coding system a University of Saint Etienne France, b University of Manchester, United Kingdom c Radboud University of Nijmegen Medical Centre,The Netherlands d University Hospitals of Geneva, Switzerland e National Centre for Classification in Health, Australia f Freiburg University Hospital, Germany g Nova University of Lisbon, Portugal rodrigues@univ-st-etienne.fr

2 MIE06 TUTORIAL USE2

3 3 Terminology to Ontology 1 Introduction 2 Definitions 3 Galen and CCAM 4 ICHI Galen 5 Discussion 6 Conclusion

4 MIE06 TUTORIAL USE4 Terminology to Ontology 1 Introduction 2 Definitions 3 Galen and CCAM 4 ICHI Galen 5 Discussion 6 Conclusion

5 MIE06 TUTORIAL USE5 ACRONYMS. 1. GALEN (Generalised Architecture for Languages, Encyclopaedias and Nomenclatures in Medicine) EU project 2. ICHI (International Classification of Health Interventions)NCCH Australia 3. CCAM (Classification Commune des Actes Médicaux) France 4. CEN standards on categorial structure 1. EN 12 264 Categorial structure 2. EN 1828 Categorial structure for surgical interventions

6 MIE06 TUTORIAL USE6 TERMINOLOGY Term + meaning Terminology artefacts ( nomenclature,flat list of controlled vocabularies,classifications and thesaurus,coding system) Used to analyse the reality from instances of universals (entities invariant in time and space) known or to know Used by humans with flexibility and ambiguity

7 MIE06 TUTORIAL USE7 FIRST GENERATION TERMINOLOGICAL SYSTEMS 1 FIRST GENERATION * presentation : systematic list(typically with codes), alphabetical index with permutations * organization : fixed (typically one, hierarchical) * purposes : devoted to a single application * flexibility NO * extension : restricted to author * processing on semantics : NO Examples : ICD9, ICD9 CM, ICD10 ICPM OPCS CDAM ICHI

8 MIE06 TUTORIAL USE8 SECOND GENERATION TERMINOLOGICAL SYSTEMS 2 SECOND GENERATION *presentation : categorial structure + cross-thesaurus + lists (classifications, nomenclatures,...) * organization : dynamic (multiple, hierarchical) * purposes : multiple * flexibility and extensions : Yes with restrictions new combinations can be made by users but without knowledge validation * processing on semantics : Yes but restricted to the predefined categorial structure Examples : SNOMED III, ICD10 PCS,CCI,CCAM LOINC-LAB, DICOM-SDM (Snomed Dicom Microglossary :imaging) MCTGE Minimum Common Terminology for Gastro intestinal Endoscopy CISP/ICPC,Braun, CIF,DSMIII and DSMIV

9 MIE06 TUTORIAL USE9 THIRD GENERATION TERMINOLOGICAL SYSTEMS 3 THIRD GENERATION * presentation : categorial structure + cross-thesaurus + lists + knowledge based model / ontology model (all and only sensible medical concepts) * organization : dynamic (multiple, hierarchical) * purposes : multiple * flexibility and extensions : unrestricted new combinations validated by knowledge base model (by predefined combinatorial rules) * processing on semantics : Yes complete (formal processing) Examples : SNOMED-RT and –CT? GALEN FMA GO

10 MIE06 TUTORIAL USE10 TERMINOLOGY and ONTOLOGY Third generation terminologies are a set of terminological artefacts related to a knowledge representation of “all and only sensible concepts-universals” in a compositional structure allowing multiple hierarchies : this representation being a type of ontology.

11 MIE06 TUTORIAL USE11 ONTOLOGY vs TERMINOLOGY Ontology :a representation of some pre-existing domain of reality (1) reflects the properties of the entities within its domain in such a way that it obtains a systematic correlation between reality and the representation itself and the non ambiguous comparison between different representations of the reality (2) is intelligible to a domain expert, (3) is formalised in a way that allows it to support automatic information processing. Distinct from Terminology

12 MIE06 TUTORIAL USE12 ONTOLOGY vs TERMINOLOGY 3 types for ontology 1 Top level/Meta Ontology 2 Domain Reference Ontology Ontology for anatomy Ontology for biology Ontology for interventions 3 Application Ontology Related to clinical terminologies Galen 1 et 2 FMA 2 GALEN-CCAM ICHI and CEN categorial structures 3 ?

13 MIE06 TUTORIAL USE13 Terminology to Ontology 1 Introduction 2 Definitions 3 Galen and CCAM 4 ICHI Galen 5 Discussion 6 Conclusion

14 MIE06 TUTORIAL USE14 Galen model A two steps approach. 1Top down modelling by -full categorisation of real world -multiple inheritance composite concepts(meaning) hierarchy -semantic relations between them -sanctions tests constraining the composition of concepts Formal language GRAIL (Galen Representation and Integration Language). 2 Bottom up extension -pragmatic reverse engineering -surgical interventions :GALEN-In-USE -centres in Belgium,Finland,France,Germany, Greece,Italy,The Netherlands,UK, Sweden - diagnostic Hungary 9400 sensible tests

15 MIE06 TUTORIAL USE15 GALEN CORE Model top level category space

16 MIE06 TUTORIAL USE16 Extended GALEN scheme for Surgical Procedure (GASP)

17 MIE06 TUTORIAL USE17 CCAM-developments CCAM development Domain experts consensus in French language (1.5 person-century) GALEN tools application Semi formal representation by junior physicians Mapping to GRAIL language GALEN formal representation Natural language processing generation to French language Conformance to European standards EN 1828 EN12 264 GALEN representation for 7478 surgical procedures 700 new concepts Using 2400 descriptors and 59 semantic links

18 MIE06 TUTORIAL USE18 CCAM- GALEN - representation 7478 rubrics of composite surgical procedures (X3) 2400 concept descriptors and 59 semantic links 2400 descriptors, 1297 descriptors for Anatomy category with 30 semantic categories 271 descriptors for Pathology category 231 descriptors for Device category 186 descriptors for Deed category 59 semantic links 27 concerning 4 categories 7 only for Pathology (motivated by,to achieve et..)

19 MIE06 TUTORIAL USE19 Linguistic and Ontology Assessments (adapted from Baud and Rassinoux) En: exeresis of an intracranial abscess by craniotomy Fr: exérèse d'un abcès intracrânien par craniotomie It: exeresi di un acesso intracranico con craniotoma Generated controlled rubric GALEN expression [GeneralisedProcess]- (playsClinicalRole)->[SurgicalRole] (isMainlyCharacterisedBy)->[performance]- (isEnactmentOf)->[Excising]- (hasSpecificSubprocess)->[Accessing]- (hasSpecificSubprocess)->[Incising]- (actsSpecificallyOn)->[Skull] (playsClinicalRole)->[SurgicalRole]\ (actsSpecificallyOn)->[BodyCavity]- (isSpaceDefinedBy) [TruelyHollowBodyStructure(isContainedIn)- >[IntracranialSpace](contains)->[Pus] (hasPathologicalStatus)->[pathological]\ (playsClinicalRole)->[SurgicalRole]\\\. Original rubric: French CCAM: Exérèse d'un abcès endocrânien par craniotomie Semiformal representation SPET Excising Acts_On Abscess is_Contained_In)->Intra cranial Space\ By approach technique Incising- Acts_On Skull. Linguistic evaluation Compositional modeling CCAM assessment Dissection GENERATOR

20 MIE06 TUTORIAL USE20 Step 1 MAKE AN INTERMEDIATE DISSECTION(claw ) 1) RUBRIQUE INITIALE U2.050 Résection endoscopique cervico-prostatique, avec urétrotomie à l’aveugle, urétrocystoscopie et mise en place d'une sonde urétrale. 2) DISSECTION INTERMEDIAIRE RUBRIC "Résection endoscopique cervico-prostatique, avec urétrotomie à l'aveugle, urétrocystoscopie et mise en place d'une sonde urétrale" SOURCE USE CODE "U2.050" MAIN resecting ACTS_ON Anatomy: neck_of_urinary_bladder & prostate BY_MEANS_OF endoscope BY_TECHNIQUE inspecting ACTS_ON Anatomy: urinary bladder & urethra BY_MEANS_OF Device : endoscope WITH_GUIDANCE_BY Device : endoscope WITH installing ACTS_ON Device: catheter HAS_DESTINATION Anatomy: urethra WITH incising ACTS_ON Anatomy: urethra HAS_APPROACH closed approach

21 MIE06 TUTORIAL USE21 3) GRAIL REPRESENTATION [cl_SurgicalDeed,[rel_isMainlyCharacterisedBy([cl_performance,[rel_isEnactment Of([cl_NLGCPT_Resecting,[rel_actsSpecificallyOn([cl_ArbitraryBodyConstruct,[rel _hasStructuralComponent(cl_UrinaryBladderNeck),rel_hasStructuralComponent(c l_ProstateGland)]]),rel_hasSpecificPhysicalMeans(cl_Endoscope),rel_hasSpecific Subprocess([cl_Inspecting,[rel_actsSpecificallyOn([cl_ArbitraryBodyConstruct,[re l_hasStructuralComponent(cl_UrinaryBladder),rel_hasStructuralComponent(cl_Ur ethra)]]),rel_hasSpecificPhysicalMeans(cl_Endoscope)]])]])]]),rel_isCharacterised By([cl_performance,[rel_isEnactmentOf([cl_NLGCPT_InstallingProcess,[rel_Locati veAttribute([cl_Catheter,[rel_isActedOnSpecificallyBy([cl_Transport,[rel_hasSpeci ficConsequence([cl_Displacement,[rel_hasBetaConnection(cl_Urethra)]])]])]])]])]]), rel_isCharacterisedBy([cl_performance,[rel_isEnactmentOf([cl_NLGCPT_Incising,[ rel_actsSpecificallyOn(cl_Urethra),rel_hasSpecificSubprocess([cl_SurgicalApproa ching,[rel_hasSurgicalOpenClosedness([cl_SurgicalOpenClosedness,[rel_hasAbs oluteState(cl_surgicallyClosed)]])]])]])]])]] Step 2 Expand to formal Representation

22 MIE06 TUTORIAL USE22 Original: résection endoscopique cervico-prostatique, avec urétrotomie à l’aveugle, urétrocystoscopie et mise en place d'une sonde urétrale Génération sans contraction : acte chirurgical de résection endoscopique d'une entité corporelle ayant pour partie le col de la vessie et ayant pour partie la prostate sous inspection endoscopique d'une entité corporelle ayant pour partie la vessie et ayant pour partie l'urètre avec mise en place d'un cathéter dans l'urètre et avec incision urétrale et fermée. Génération avec contraction : résection sous endoscope du col de la vessie et de la prostate avec inspection endoscopique de l’urètre et de la vessie avec incision fermée de l’urètre et mise en place d’un cathéter dans l’urètre Step 3 Controlled natural language generation (see S Hansen Freiburg)

23 MIE06 TUTORIAL USE23 What is an arthroplasty ? installing a prosthesis within the joint to replace at least a part of it R0232b Arthroplastie du poignet par prothèse partielle, à ciel ouvert R0847 Arthroplastie inter somatique par prothèse discale R1285b Reconstruction de l'articulation du genou par prothèse massive ou sur mesure, après perte de substance segmentaire.Avec ou sans : reconstruction de l'appareil extenseur R0064 Arthroplastie scapulo humérale par prothèse humérale unipolaire ou par cupule mobile R0231 Arthroplastie radio carpienne par prothèse totale à ciel ouvert R0403 Arthroplastie coxo-fémorale par cupule fémorale QA with ontology driven tools:

24 MIE06 TUTORIAL USE24 What is an arthroplasty ? installing a prosthesis within the joint to replace at least a part of it or A plastic repairing of the components of a joint Without installing a prosthesis to replace the joint? R0290b Arthroplastie de plusieurs articulations d'un rayon de la main R0289b Arthroplastie d'une articulation d'un rayon de la main.A l'exclusion de : arthroplastie de l'articulation carpo-métacarpienne du pouce R0233 Arthroplastie de l’articulation carpo-métacarpienne du pouce avec ou sans plastie de l’appareil capsulo ligamentaire QA with ontology driven tools:

25 MIE06 TUTORIAL USE25 Terminology to Ontology 1 Introduction 2 Definitions 3 Galen and CCAM 4 ICHI Galen 5 Discussion 6 Conclusion

26 MIE06 TUTORIAL USE26 ICHI GALEN METHOD Semi formal representation using SPET (Kermanog Inc) by University of Saint Etienne (France) Radboud University Nijmegen (The Netherlands) Mapping to GRAIL language GALEN formal representation University of Manchester (UK) Natural Language Processing generation to English, Portuguese and French languages University Hospitals of Geneva (Switzerland) University of Freiburg (Germany) Conformity to European Standards EN 1828 and EN 12264

27 MIE06 TUTORIAL USE27 initial rubric : ICHI-Chapter XV,1518 Arthroplasty of knee generated label : En :Repairing of the knee joint. Po:Reparação da articulacâo do joelho. Fr: Réparation de l’articulation du genou. QA with ontology driven tools What is an arthroplasty ? A plastic repairing of the components of a joint without installing a prosthesis to replace the joint? Code 1518

28 MIE06 TUTORIAL USE28 initial rubric : ICHI-Chapter XV,1519 Arthroplasty of knee with bone graft to femur or tibia generated label : En :Replacement of the knee joint with a prosthesis of the knee joint,with installation of bone graft tissue in the femur or the tibia by means of harvesting bone. Po:Substituição da articulacâo do joelho cum una prótese da articulacâo do joelho, cum instalacão de transplante de tecido de osso no fémur ou na tíbia por meio de colhida do osso. Fr: Remplacement de l’articulation du genou par une prothèse de l’articulation du genou avec mise en place de tissu osseux greffé sur le fémur ou le tibia au moyen de prélèvement osseux. QA with ontology driven tools What is an arthroplasty ? installing a prosthesis within the joint to replace at least a part of it code 1519

29 MIE06 TUTORIAL USE29 initial rubric : ICHI-Chapter XV,1589 Arthroplasty of hip joint generated label : En :Repairing of the hip joint. Plastic repairing or Hip replacement with a prosthesis? Po:Reparação da articulacâo do anca/quadril. Reparação plástico ou Substituição da articulacâo do anca cum una prótese ? Fr: Réparation de l’articulation de la hanche. Réparation plastique ou Prothèse de hanche? QA with ontology driven tools What is an arthroplasty ? Code 1589

30 MIE06 TUTORIAL USE30 Terminology to Ontology 1 Introduction 2 Definitions 3 Galen and CCAM 4 ICHI Galen 5 Discussion 6 Conclusion

31 MIE06 TUTORIAL USE31 GALEN-CCAM lessons (coordination terminology ontology) Coordination of terminology and ontology has allowed participation of clinical experts colleges in their natural language (bottom up) Has Mixed contradictory trends Terminology artefacts aligned to evidence rather than God belief Supporting contradiction To allow linguistic ambiguity monitoring for humans Description logic is necessary for machine:computers Different end users goals need different terminology artefacts

32 MIE06 TUTORIAL USE32 ICHI GALEN 3 goals to 4  To demonstrate that a compositional approach to developing WHO candidate terminologies is feasible and cost-effective ;  To demonstrate a more collaborative approach to building international terminologies, including open developments (OpenGalen);  To demonstrate that automatic translations based on an ontology make the translation process more transparent faster and of better quality ;  To provide evidence on comparative costs with the traditional domain experts method to inform future decision making ?

33 MIE06 TUTORIAL USE33 Terminology to Ontology 1 Introduction 2 Definitions 3 Galen and CCAM 4 ICHI Galen 5 Discussion 6 Conclusion

34 MIE06 TUTORIAL USE34 CONCLUSION 1 This work has demonstrated the feasibility to apply ontology driven tools designed for a national coding system (French CCAM) within a EU funded project and a collaborative approach to the development of a terminology ICHI candidate to become the WHO classification of health interventions. Such a method has shown 20 % inconsistencies in traditional coding systems and convinced international and national organisations that it was a better and easier method to maintain and to share coding systems between countries than the traditional domain experts consensus method used until now.

35 MIE06 TUTORIAL USE35 CONCLUSION It is still necessary to convince the decision makers that it can be faster and cheaper by multiplying the number of modelling centres working in their local language and investing in few web based tools platforms than in the traditional bottomless domain expertise. As the healthcare systems are becoming more and more knowledge-based and communicating the terminology they use must be able to allow their expressiveness and in a sense their ambiguity but must be constrained by a formal logic representation or ontology based within the computer to insure the safety of healthcare delivery. The process we have developed for classifications and coding systems shall be tested for any clinical terminology (Snomed CT?).

36 MIE06 TUTORIAL USE36 ENDE Vielen Dank für Ihre Aufmerksamkeit Thank you MerciGracieGraciasObligadoEfcharisto ARIGATO GOZAIMASU Tag Multumesc.


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