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Ontology-Driven Collaborative Development for Biomedical Terminologies

Explore how French CCAM is transformed into the Australian ICHI coding system using ontology-driven collaborative development. Discuss Galen and ICHI Galen, and their implications.

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Ontology-Driven Collaborative Development for Biomedical Terminologies

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  1. 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 MIE06 TUTORIAL USE

  2. MIE06 TUTORIAL USE

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

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

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

  6. 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 MIE06 TUTORIAL USE

  7. 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 MIE06 TUTORIAL USE

  8. 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 MIE06 TUTORIAL USE

  9. 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 MIE06 TUTORIAL USE

  10. 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 . MIE06 TUTORIAL USE

  11. 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 MIE06 TUTORIAL USE

  12. 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 ? MIE06 TUTORIAL USE

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

  14. 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 MIE06 TUTORIAL USE

  15. GALEN CORE Model top level category space MIE06 TUTORIAL USE

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

  17. 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 MIE06 TUTORIAL USE

  18. 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..) MIE06 TUTORIAL USE

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

  20. 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 MIE06 TUTORIAL USE

  21. Step 2Expand to formal Representation 3) GRAIL REPRESENTATION [cl_SurgicalDeed,[rel_isMainlyCharacterisedBy([cl_performance,[rel_isEnactmentOf([cl_NLGCPT_Resecting,[rel_actsSpecificallyOn([cl_ArbitraryBodyConstruct,[rel_hasStructuralComponent(cl_UrinaryBladderNeck),rel_hasStructuralComponent(cl_ProstateGland)]]),rel_hasSpecificPhysicalMeans(cl_Endoscope),rel_hasSpecificSubprocess([cl_Inspecting,[rel_actsSpecificallyOn([cl_ArbitraryBodyConstruct,[rel_hasStructuralComponent(cl_UrinaryBladder),rel_hasStructuralComponent(cl_Urethra)]]),rel_hasSpecificPhysicalMeans(cl_Endoscope)]])]])]]),rel_isCharacterisedBy([cl_performance,[rel_isEnactmentOf([cl_NLGCPT_InstallingProcess,[rel_LocativeAttribute([cl_Catheter,[rel_isActedOnSpecificallyBy([cl_Transport,[rel_hasSpecificConsequence([cl_Displacement,[rel_hasBetaConnection(cl_Urethra)]])]])]])]])]]),rel_isCharacterisedBy([cl_performance,[rel_isEnactmentOf([cl_NLGCPT_Incising,[rel_actsSpecificallyOn(cl_Urethra),rel_hasSpecificSubprocess([cl_SurgicalApproaching,[rel_hasSurgicalOpenClosedness([cl_SurgicalOpenClosedness,[rel_hasAbsoluteState(cl_surgicallyClosed)]])]])]])]])]] MIE06 TUTORIAL USE

  22. Step 3Controlled natural language generation (see S Hansen Freiburg) 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 MIE06 TUTORIAL USE

  23. QA with ontology driven tools: 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 MIE06 TUTORIAL USE

  24. QA with ontology driven tools: 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 MIE06 TUTORIAL USE

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

  26. 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 MIE06 TUTORIAL USE

  27. QA with ontology driven toolsWhat is an arthroplasty ?A plastic repairing of the components of a joint without installing a prosthesis to replace the joint?Code 1518 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. MIE06 TUTORIAL USE

  28. 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 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 deosso 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. MIE06 TUTORIAL USE

  29. QA with ontology driven tools What is an arthroplasty ?Code 1589 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? MIE06 TUTORIAL USE

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

  31. 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 MIE06 TUTORIAL USE

  32. 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 ? MIE06 TUTORIAL USE

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

  34. 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. MIE06 TUTORIAL USE

  35. 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?). MIE06 TUTORIAL USE

  36. ENDE Vielen Dank für Ihre Aufmerksamkeit Thank you Merci Gracie Gracias Obligado Efcharisto ARIGATO GOZAIMASU Tag Multumesc. MIE06 TUTORIAL USE

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