IMIA Working Group 6 Medical Concept Representation

2. IMIA Working Group 6 Medical Concept Representation Focus of Meeting: • New role of ontological research • for new age of biomedical informatics Scientific developments: foundational issues rather than operational questions • Long-term view: • ensure development of robust • biomedical ontologies for the future

3. IMIA Working Group 6 Medical Concept Representation The Foundational Role of Anatomy for Biomedical Ontologies Cornelius Rosse M.D., D.Sc. S t r u c t u r a l I n f o r m a t i c s G r o u p University of Washington

4. What will be the take home message? What are the problems? We have established biomedical informatics Is it a service? Is it a new biomedical science? If a science What is its theoretical foundation? What is its methodology? Are theory and ontological methodology applied in the practice of biomedical informatics? How do applications of theory and methodology supportinference about individuals (EHR)?

5. What will be the take home message? What are the solutions? • Theoretical solution • Propose a theory for biomedical reality • derived from top-level ontologies • Methodological solution • Develop reference ontologies in • domains of empirical basic biomedical science • using sound methodology • Reuse reference ontologies in • application ontologies designed for • clinical specialties • biomedical research • education and training

6. Case study: Cardiac Cycle

7. Case study: Cardiac Cycle

8. Case study: Cardiac Cycle Atrial pressure

9. Case study: Cardiac Cycle Left ventricular pressure Atrial pressure

10. Case study: Cardiac Cycle Left ventricular pressure Left ventricular volume Atrial pressure

11. Case study: Cardiac Cycle Left ventricular pressure Aortic pressure Left ventricular volume Atrial pressure

12. Case study: Cardiac Cycle Left ventricular pressure Aortic pressure Left ventricular volume Atrial pressure

13. Case study: Cardiac Cycle Left ventricular pressure Aortic pressure Left ventricular volume Atrial pressure

14. Movie

15. Case study: Cardiac Cycle Task: Generate ontological representation Resources extant terminologies: UMLS

16. Cardiac Cycle in UMLS

17. Cardiac Cycle in UMLS

18. Cardiac Cycle in UMLS

19. Cardiac Cycle in UMLS

20. Movie

21. Case study: Cardiac Cycle Task: Generate ontological representation of cardiac cycle Resources extant terminologies: UMLS textbooks, literature re-examination of cardiac cycle from ontological perspective

22. Diversion! Task: Generate ontological representation of cardiac cycle Resources extant terminologies: UMLS textbooks, literature re-examination of cardiac cycle from ontological perspective

23. Constitutents of Medical Science Basic sciences Clinical sciences

24. Constituents of Medical Science Basic sciences Clinical sciences Physiology Internal medicine Pathology Pediatrics Microbiology Psychiatry Biochemistry Anesthesiology Anatomy Surgery macroscopic general surgery microscopic maxillofacial surgery embryology otolaryngology neuroanatomy neurosurgery

25. Basic Sciences Characteristics Taught/learned during first phase of professional training Concerned with canonical knowledge not data pertaining to individuals Do not target specialties in clinical medicine Need to be relearned in context of medical specialties Purpose Provide general understanding for reasoning and managing data pertaining to individuals

26. Basic Sciences Changing Environment 1960’s: curricular reform 1970’s: new biology

27. Basic Sciences Changing Environment 1960’s: curricular reform 1970’s: new biology Medicine Biomedicine; Biomedical science

28. Constituents of Biomedical Science Basic sciences Clinical sciences Physiology Internal medicine Pathology Pediatrics Microbiology Psychiatry Biochemistry Anesthesiology Anatomy Surgery macroscopic general surgery microscopic maxillofacial surgery embryology otolaryngology neuroanatomy neurosurgery Traditional disciplines New biologyNew medicine molecular and cell biology molecular medicine genomics, proteomics regenerative medicine developmental biology translational medicine systems biology nuclear medicine

29. What is Biomedical Informatics? Basic sciences Clinical sciences Physiology Internal medicine Pathology Pediatrics Microbiology Psychiatry Biochemistry Anesthesiology Anatomy Surgery macroscopic general surgery microscopic maxillofacial surgery embryology otolaryngology neuroanatomy neurosurgery Traditional disciplines New biologyNew medicine molecular and cell biology molecular medicine genomics, proteomics regenerative medicine developmental biology translational medicine systems biology nuclear medicine Biomedical Informatics

30. What will be the take home message? What are the problems? We have established biomedical informatics Is it a service? Is it a new biomedical science? If a science What is its theoretical foundation? What is its methodology? Are theory and ontological methodology applied in the practice of biomedical informatics? How do applications of theory and methodology supportinference about individuals (EHR)?

31. Attributes of Science Science has a.) theories on basis of which hypotheses can be formulated b.) methodology which can test the hypotheses Best hope: Ontology

32. Need for theories and methodology What is ontology ? Smith (1996): “the science which deals with the nature and organization of reality” Grenon, Smith & Goldberg (2004) “An ontology grasps the entities which exist within a given portion of the world at a given level of generality. It includes a taxonomy of the types of entities and relations that exist in that portion of the world seen from a given perspective.” Ontological theories derive from the philosophy of reality Ontological methodology creates an artifact which depicts a portion of the world seen from a given perspective

33. Need for theories and methodology What is ontology ? first meaning: Smith (1996): “the science which deals with the nature and organization of reality Grenon, Smith & Goldberg (2004) “An ontology grasps the entities which exist within a given portion of the world at a given level of generality. It includes a taxonomy of the types of entities and relations that exist in that portion of the world seen from a given perspective.” second meaning: an artifact projects to a given domain of reality created through the application of principles and methods of ontological science

34. Why base an ontology on reality? Ambiguity • any domain discourse is full with it • humans are adapt at dealing with it - printed page tolerates it • computational inference will be crippled by it

35. Why base an ontology on reality? Ambiguity • any domain discourse is full with it • humans are adapt at dealing with it - printed page tolerates it • computational inference will be crippled by it Conclusion: - we have to base ontology on reality - need to take a new look at reality

36. What kinds of ontologies are there? • Formal, top-level ontologies • 2. Domain reference ontologies • 3. Terminology-based application ontologies

37. What kinds of ontologies are there? • Formal, top-level ontologies:DOLCE, BFO • domain-independent theories • framework of axioms and definitions • high degree of representational accuracy • designed to be used as controls on other types of ontologies

38. What kinds of ontologies are there? • Formal, top-level ontologies:DOLCE, BFO • domain-independent theories • framework of axioms and definitions • high degree of representational accuracy • designed to be used as controls on other types of ontologies • 2. Domain reference ontologies:FMA • declare a theory about a particular domain of reality • make use of methods of top-level ontologies • general purpose resources • generalize to other domains • anatomy generalizes to physiology, surgery

39. What kinds of ontologies are there? • Formal, top-level ontologies:DOLCE, BFO • domain-independent theories • framework of axioms and definitions • high degree of representational accuracy • designed to be used as controls on other types of ontologies • 2. Domain reference ontologies:FMA • declare a theory about a particular domain of reality • make use of methods of top-level ontologies • general purpose resources • generalize to other domains • anatomy generalizes to physiology, surgery • 3. Terminology-based application ontologies: • GO, other OBO, SNOMED, MeSH • systems of terms • purpose-built • designed to meet particular needs • annotating databases, medical data

40. Basic Formal Ontology Entities Occurrents Continuants Distinguishing criterion (differentia): Time

41. Basic Formal Ontology Entities Occurrents- SPAN entities Dependent entities which do not endure through time; unfold themselves in successive temporal phases (e.g., processes, actions) have temporal parts

42. Basic Formal Ontology Entities Occurrents- SPAN entities Dependent entities which do not endure through time; unfold themselves in successive temporal phases (e.g., processes, actions) have temporal parts Continuants - SNAP entities Entities which endurein toto in every instant of time at which they exist have spatial parts Independent continuants objects, components Dependent continuants attributes, roles, qualities, functions

43. END OF DIVERSION

44. A theory of biomedical reality Biological entity Biological continuant Biological occurrent is-a

45. Biological entity Biological continuant Biological occurrent is-a Extra-organismal biological continuant Organismal continuant

46. Biological entity Biological continuant Biological occurrent is-a Extra-organismal biological continuant Organismal continuant Independent organismal continuant Dependent organismal continuant

47. Biological entity Biological continuant Biological occurrent is-a Extra-organismal biological continuant Organismal continuant Independent organismal continuant Dependent organismal continuant Material anatomical entity Material pathological entity Anatomical structure Canonical anatomical structure Variant anatomical structure Portion of canonical body substance Portion of blood Portion of cytosol Pathological structure Neoplasm Inflammatory structure Degenerated structure Portion of pathological body substance Portion of pus Portion of amyloid

48. Biological entity Biological continuant Biological occurrent is-a Extra-organismal biological continuant Organismal continuant Independent organismal continuant Dependent organismal continuant Material anatomical entity Material pathological entity Immaterial anatomical continuant Physiological continuant Immaterial pathological continuant Anatomical structure Canonical anatomical structure Variant anatomical structure Portion of canonical body substance Portion of blood Portion of cytosol Pathological structure Neoplasm Inflammatory structure Degenerated structure Portion of pathological body substance Portion of pus Portion of amyloid Anatomical space Cavity of lysosome Anatomical surface E-face of plasma membrane Anatomical line Anatomical point Function Secrete Flex; Extend Physiological state Relaxed state Contracted state Physiological role Antagonist Pathological space Cavity of abscess Pathological surface Boundary of tumor Malfunction Atrial fibrillation Pathological state Malnutrition Pathological role

49. Biological entity Biological continuant Biological occurrent is-a Extra-organismal biological continuant Organismal continuant Extra-organismal biological occurrent Organismal occurrent Independent organismal continuant Dependent organismal continuant Material anatomical entity Material pathological entity Immaterial anatomical continuant Physiological continuant Immaterial pathological continuant Anatomical structure Canonical anatomical structure Variant anatomical structure Portion of canonical body substance Portion of blood Portion of cytosol Pathological structure Neoplasm Inflammatory structure Degenerated structure Portion of pathological body substance Portion of pus Portion of amyloid Anatomical space Cavity of lysosome Anatomical surface E-face of plasma membrane Anatomical line Anatomical point Function Secrete Flex; Extend Physiological state Systole Physiological role Antagonist Pathological space Cavity of abscess Pathological surface Boundary of tumor Malfunction Atrial fibrillation Pathological state Malnutrition Pathological role

50. Biological entity Biological continuant Biological occurrent is-a Extra-organismal biological continuant Organismal continuant Extra-organismal biological occurrent Organismal occurrent Independent organismal continuant Dependent organismal continuant Physiological process Pathological process Secreting Secreting insulin Transcribing RNA Mutating Metastasizing Necrosing Material anatomical entity Material pathological entity Immaterial anatomical continuant Physiological continuant Immaterial pathological continuant Anatomical structure Canonical anatomical structure Variant anatomical structure Portion of canonical body substance Portion of blood Portion of cytosol Pathological structure Neoplasm Inflammatory structure Degenerated structure Portion of pathological body substance Portion of pus Portion of amyloid Anatomical space Cavity of lysosome Anatomical surface E-face of plasma membrane Anatomical line Anatomical point Function Secrete Flex; Extend Physiological state Systole Physiological role Antagonist Pathological space Cavity of abscess Pathological surface Boundary of tumor Malfunction Atrial fibrillation Pathological state Malnutrition Pathological role