Werner CEUSTERS, MD

1. IADR Satellite SymposiumOntology: Innovative Approach to Orofacial Pain ClassificationMarch 19, 2013 – Washington State Convention Center, Seattle, WA Werner CEUSTERS, MD Center of Excellence in Bioinformatics and Life Sciences, Ontology Research Group, Institute for Healthcare Informatics, Department of Psychiatry University at Buffalo, NY, USA http://www.org.buffalo.edu/RTU

2. A classification of animals Celestial Emporium of Benevolent Knowledge's Taxonomy • Those that belong to the emperor • Embalmed ones • Those that are trained • Suckling pigs • Mermaids (or Sirens) • Fabulous ones • Et cetera • Those that are included in this classification • Those that tremble as if they were mad • Innumerable ones • Those drawn with a very fine camel hair brush • Stray dogs • Those that have just broken the flower vase • Those that, at a distance, resemble flies Jorge Luis Borges. The Analytical Language of John Wilkins. 1942. (Selected nonfictions, Eliot Weinberger, transl., Penguin Books, p. 231, ISBN 0-14-029011-7)

3. A classification of animals Celestial Emporium of Benevolent Knowledge's Taxonomy • Those that belong to the emperor • Embalmed ones • Those that are trained • Suckling pigs • Mermaids (or Sirens) • Fabulous ones • Et cetera • Those that are included in this classification • Those that tremble as if they were mad • Innumerable ones • Those drawn with a very fine camel hair brush • Stray dogs • Those that have just broken the flower vase • Those that, at a distance, resemble flies Ridiculous? Jorge Luis Borges. The Analytical Language of John Wilkins. 1942. (Selected nonfictions, Eliot Weinberger, transl., Penguin Books, p. 231, ISBN 0-14-029011-7)

4. Africa [Z01.058] + Americas [Z01.107] + Antarctic Regions [Z01.158] Arctic Regions [Z01.208] Asia [Z01.252] + Atlantic Islands [Z01.295] + Australia [Z01.338] + Cities [Z01.433] + Europe [Z01.542] + Historical Geographic Locations [Z01.586] + Indian Ocean Islands [Z01.600] + Oceania [Z01.678] + Oceans and Seas [Z01.756] + Pacific Islands [Z01.782] + Ancient Lands [Z01.586.035] + Austria-Hungary [Z01.586.117] Commonwealth of Independent States [Z01.586.200] + Czechoslovakia [Z01.586.250] + European Union [Z01.586.300] Germany [Z01.586.315] + Korea [Z01.586.407] Middle East [Z01.586.500] + New Guinea [Z01.586.650] Ottoman Empire [Z01.586.687] Prussia [Z01.586.725] Russia (Pre-1917) [Z01.586.800] USSR [Z01.586.950] + Yugoslavia [Z01.586.980] + Geographic Locations [Z01] in MESH ? ? ?

5. All MeSH Categories Diseases Category Nervous System Diseases Female Urogenital Diseases and Pregnancy Complications Male Urogenital Diseases Eye Diseases Cranial Nerve Diseases Female Urogenital Diseases Neurodegenerative Diseases Optic Nerve Diseases Optic Nerve Diseases Urologic Diseases Heredodegenerative Disorders, Nervous System Eye Diseases, Hereditary Optic Atrophy Kidney Diseases Optic Atrophies, Hereditary Diabetes Insipidus Wolfram Syndrome MeSH: some paths from top to Wolfram Syndrome

6. All MeSH Categories ??? Diseases Category Nervous System Diseases Female Urogenital Diseases and Pregnancy Complications Male Urogenital Diseases Eye Diseases Cranial Nerve Diseases Female Urogenital Diseases … Neurodegenerative Diseases Optic Nerve Diseases Optic Nerve Diseases Urologic Diseases Heredodegenerative Disorders, Nervous System Eye Diseases, Hereditary has Optic Atrophy Kidney Diseases Optic Atrophies, Hereditary Diabetes Insipidus Wolfram Syndrome What would it mean if used in the context of a patient ? has

7. Ridiculous ? Celestial Emporium of … Pain classification • Those that belong to the emperor • Embalmed ones • Those that are trained • Suckling pigs • Mermaids (or Sirens) • Fabulous ones • Et cetera • Those that are included in this classification Peripheral Neuropathy (I-1) 203.X2a Arms: infective 203.X3a Arms: inflammatory or immune reactions 203.X5a Arms: toxic, metabolic, etc. 203.X8a Arms: unknown or other 603.X2a Legs: infective 603.X3a Legs: inflammatory or immune reactions 603.X5a Legs: toxic, metabolic, etc. 603.X8a Legs: unknown or other X03.X4d Von Recklinghausen's disease

8. Why ridiculous? Non-systematic criteria. reference to external characteristic not animal anymore temporal characteristic do not exist at all ambiguous open ended reference to observer • Those that belong to the emperor • Embalmed ones • Those that are trained • Suckling pigs • Mermaids (or Sirens) • Fabulous ones • Et cetera • Those that are included in this classification • Those that, at a distance, resemble flies

9. 7 criteria for a good term: Transparency: to make the term transparent, a delimiting characteristic is used to create the term Consistency: within a concept system Appropriateness: adhere to establish patterns, avoid confusion Linguistic economy Derivability Compoundability Linguisticcorrectness Preference for native language. A first stab at systematization: Terminology ISO 704, 2000

10. Application in healthcare: Cimino’s desiderata

11. 7 criteria for a good term: Transparency: to make the term transparent, a delimiting characteristic is used to create the term Consistency: within a concept system Appropriateness: adhere to establish patterns, avoid confusion Linguistic economy Derivability Compoundability Linguistic correctness Preference for native language. The weakness of terminology ISO 704, 2000

12. The wobbly foundations of concept theories

13. A better way to systematize: ‘Ontology’ • In philosophy: • Ontology(no plural) is the study of what entities exist and how they relate to each other; • by some philosophers taken to be synonymous with ‘metaphysics’ while others draw distinctions in many distinct ways(the distinctions being irrelevant for this talk), but almost agreeing on the following classification: • metaphysics  studies ‘how is the world?’ • general metaphysics  studies general principles and ‘laws’ about the world • ontology  studies what type of entities exist in the world • special metaphysics  focuses on specific principles and entities • distinct from ‘epistemology’ which is the study of how we can come to know about what exists. • distinct from ‘terminology’ which is the study of what terms mean and how to name things.

14. A better way to systematize: ‘Ontology’ • In philosophy: • Ontology(no plural) is the study of what entities exist and how they relate to each other; • In computer science and many biomedical informatics applications: • An ontology(plural: ontologies) is a shared and agreed upon conceptualization of a domain;

15. Computer science approach to ontology Ontology Authoring Tools create Reasoners Domain Ontologies Semantic Applications use

16. Computer science approach to ontology Ontology Authoring Tools create • the logic in reasoners: • guarantees consistent reasoning, • does not guarantee the faithfulness of the representation. Reasoners Domain Ontologies Semantic Applications use

17. Consistent reasoning with nonsensical representations Ceusters W, Smith B, Flanagan J. Ontology and Medical Terminology: why Descriptions Logics are not enough. Proceedings of the conference Towards an Electronic Patient Record (TEPR 2003), San Antonio, 10-14 May 2003 (electronic publication 5pp)

18. Philosophical approach to ontology Ontological Realism: uses ontology as philosophical discipline to build ontologies as faithful representations of reality.

20. The basis of Ontological Realism (O.R.) • There is an external reality which is ‘objectively’ the way it is; • That reality is accessible to us; • We build in our brains cognitive representations of reality; • We communicate with others about what is there, and what we believe there is there. Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, Biomedical Ontology in Action, November 8, 2006, Baltimore MD, USA

21. Ontology  Terminology reality language knowledge

22. Ontological Realism makes three crucial distinctions • Between data and what data are about; • Between continuants and occurrents; • Between what is generic and what is specific. Smith B, Ceusters W. Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies. Applied Ontology, 2010;5(3-4):139-188.

23. L3 Linguistic representations about (L1-), (L2) or (L3) Representations L2 Beliefs about (1) First Order Reality Entities (particular or generic) with objective existence which are not about anything L1-

24. L1/L2/L3 and pain • IASP definition for ‘pain’: • ‘an unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage’; • what asserts: • a common phenomenology (‘unpleasant sensory and emotional experience’) to all instances of pain, • the recognition of three distinct subtypes of pain involving, respectively: • actual tissue damage, • what is called ‘potential tissue damage’, and • a description involving reference to tissue damage whether or not there is such damage.

25. ICHD my EHR DIAGNOSIS my doctor’s work plan my doctor’s diagnosis INDICATION my doctor’s computer my doctor PATHOLOGICAL STRUCTURE PERSON me my migraine DISEASE DRUG my headache MIGRAINE HEADACHE MOLECULE Basic Formal Ontology Referent Tracking Between ‘generic’ and ‘specific’ Generic Generic Specific Specific L3. Representation pain classification EHR L2. Beliefs (knowledge) L1. First-order reality

26. Example: Ontology of General Medical Science (OGMS) produces bears realized_in etiological process disorder disease pathological process produces diagnosis interpretive process signs & symptoms abnormal bodily features produces participates_in recognized_as Scheuermann R, Ceusters W, Smith B. Toward an Ontological Treatment of Disease and Diagnosis. 2009 AMIA Summit on Translational Bioinformatics, San Francisco, California, March 15-17, 2009;: 116-120. http://www.referent-tracking.com/RTU/sendfile/?file=AMIA-0075-T2009.pdf http://code.google.com/p/ogms/

27. No conflation of diagnosis, disease, and disorder The diagnosis is here The disorder is there The disease is there

28. Some principles for O.R.-based classifications • P1: Be explicit whether assertions are about particulars or types • P2: Be precise about the sort of particulars to be classified using the classification • P3: Particulars that correctly can be classified at a certain class level, and thus are instances of the corresponding type, should also be instance of all the types that correspond with higher level classes. • P4: Keep knowledge separate from what the knowledge is about. • P5: Class descriptions should be consistent with class labels. • P6: Use Aristotelian definitions. • P7: Clinical criteria do not replace Aristotelian definitions. Are all violated in new (draft of?) Chapter 13 of ICHD

29. (P1) Are assertions about particulars or types? • ‘Persistent idiopathic facial pain (PIFP)’ = ‘persistent facial pain with varying presentations …’ persistent facial pain presentation type1 presentation type2 presentation type3 types t3 t2 t1 t1 t1 t2 t2 t3 t3 t1 t1 parti- culars t2 t1 t2 t2 t3 t3 t3 my pain her pain his pain

30. (P1) Are assertions about particulars or types? • ‘Persistent idiopathic facial pain (PIFP)’ = ‘persistent facial pain with varying presentations …’ • if the description is about types, then the threeparticularpains fall under PIFP. • if the description is about (arbitrary) particulars, then only her pain falls under PIFP.

31. (P2) Sort of particulars to be classified • What is classified in ICHD? • disorders? ‘The International Classification of Headache Disorders’ • headaches? ‘Many questions not needed in order to classify primary headaches…’ • patients? ‘The second edition will hopefully further promote unity in the way we classify, diagnose and treat headache patients throughout the world.’ • palsies? • syndromes? can be assumed from some heading names

32. (P3) Maintain a strict subsumption hierarchy • 13.1. Trigeminal Neuralgia • 13.1.2 Painful Trigeminal Neuropathy • ICHD definitions: • ‘neuralgia’ = pain in the distribution of nerve(s) • ‘pain’ = a sensorial and emotional experience ... • ‘neuropathy’= a disturbance of function or pathological change in a nerve. • Several mismatches: • (1) and (2): neuralgia is a sensorial and emotional experience in the distribution of nerve(s) ? • (1) and (3): with much of goodwill, one could accept neuropathy to subsume neuralgia, but chapter 13 claims the opposite for the trigeminal case. subsumes?

33. bones nose fracture P3-related mistake: false synonymy in SNOMED

34. A patient with a fractured nasal bone = A patient with a broken nose = A patient with a fracture of the nose Coding / Classification confusion

35. A patient with a fractured nasal bone A patient with a fractured nasal bone = = A patient with a broken nose A patient with a broken nose = = A patient with a fracture of the nose A patient with a fracture of the nose Coding / Classification confusion

36. (P4) Separate knowledge from what it is about. • ‘13.1.2.4 Painful trigeminal neuropathy attributed to MS plaque’ • ‘attributed to’ relates to somebody’s opinion about what is the case, not to what is the case. • the mistake: a feature on the side of the clinician – his (not) knowing - is taken to be a feature on the side of the patient. • Similar mistakes: • ‘Probable migraine’ • ‘facial pain of unknown origin’ (not in ICHD).

37. (P5) Class descriptions should be consistent with class labels • ‘13.1.2.4 Painful Trigeminal neuropathy attributed to MS plaque’: • described as ‘Trigeminal neuropathy induced by MS plaque’. • attributed  induced • reference to pain missing in the description

38. (P6) Use Aristotelian definitions. • A B isa A which X C isa B which Y D isa C which Z • Make sure that X holds for C and that both X and Y hold for D. • Use this also in label formation to prevent, f.i., • ‘13.3 Nervus Intermedius (Facial Nerve) Neuralgia’ ‘13.3.2. Secondary Nervus Intermedius Neuropathy attributed to Herpes Zoster’

39. (P7) Clinical criteria do not replace Aristotelian definitions • ‘13.1.1.1 Classical trigeminal neuralgia, purely paroxysmal’, has the criterion ‘at least three attacks of facial pain fulfilling criteria B-E’. • This does not mean: a patient with 2 such attacks does not exhibit this type of neuralgia; • It rather means: do not diagnose the patient (yet) as exhibiting this type of neuralgia. • If ‘chronic pain’ is defined as ‘pain lasting longer than three months’, at what point in time starts a patient to have that type of pain?

40. Conclusion • Realism-based ontology has a lot to offer to build faithful representations. • It is hard ! • Pain classifications, and as thus far ALL OTHER classifications made by domain experts, would benefit from it. • domain experts are not ontologists. • Old habits, main stream thinking, and guru-ism hamper the advance of science.

41. Acknowledgement The work described is funded in part by grant 1R01DE021917-01A1 from the National Institute of Dental and Craniofacial Research (NIDCR). The content of this presentation is solely the responsibility of the author and does not necessarily represent the official views of the NIDCR or the National Institutes of Health.