Die Ontologie biomedizinischer Daten

1. Die Ontologie biomedizinischer Daten Barry Smith Institute for Formal Ontology and Medical Information Science ifomis.org

2. IFOMIS • Institute for Formal Ontology and Medical Information Science • Mission: to develop formal ontologies to support empirical research in biomedical informatics and in the life sciences in general ifomis.org

3. Biomedical ontologies and terminology systems • currently manifest a very low degree of formal rigour ifomis.org

4. SNOMED-CT • 900,000 ‘concepts’ and relations between them, such as • is_a (for class subsumption) • part_of • causes • treats ifomis.org

5. SNOMED’s confused treatment of is_a • beide_Hoden is_a Hoden • beide_ Gebärmuttern is_a Gebärmutter ifomis.org

6. Halbextraktion_aus_Steißlage is_a Extraktion_aus_Steißlage • Extraktion_aus_Steißlageis_a vollständige_Steißgeburt • ____________________________ • Halbextraktion_aus_Steißlage is_a vollständige_Steißgeburt ifomis.org

7. Confused treatment of objects and processes • diagnostische_endoskopische_Untersuchung_eines_Mediastinums_NOS • is_a Mediastinoskop. ifomis.org

8. Confusion of object with knowledge about object • Kontrazeption is_a funktionaler_Befund ifomis.org

9. National Cancer InstituteThesaurus • a biomedical thesaurus created specifically to meet the needs of the NCI • semantically modeled cancer-related terminology built usingDescription Logic ifomis.org

10. Anatomic Structure, Anatomic System, or Anatomic Substance ? Or ? Does the NCI not know to which category Any item classified there belongs ? Anatomic Substance ? If yes, why is gene product not subsumed by it ? If no, why are drugsandchemicals not subsumed by it ? NCI Thesaurus root concepts ifomis.org

11. Conceptual entity • Definition: none • Semantic type: • Conceptual entity • Classification • Subconcepts: • Action: • definition: action; a thing done • And: • Definition: an article which expresses the relation of connection or addition, used to conjoin a word with a word, ... ifomis.org

12. Conceptual entity • Action is_a Conceptual Entity • And is_a Conceptual Entity • Swimming is healthy and contains 8 letters ifomis.org

13. Definition of “cancer gene” ifomis.org

14. What diseases have a diameter of over 3 cm ? NCI Thesaurus architecture Findings-And- Disorders-Kind Anatomy-Kind Disease “Formal subsumption” or “inheritance” “Associative” relationships providing “differentiae” “Kinds” restrict the domain and range of associative relationships ISA Breast neoplasm Breast Disease-has-associated-anatomy ifomis.org

15. Confusion of objects and the states in which they participate Findings-And- Disorders-Kind Anatomy-Kind Disease ISA Breast neoplasm Breast Disease-has-associated-anatomy ifomis.org

16. No one knows what ‘concept’ (or ‘conceptualization’) means • The linguistic reading • The psychological reading • The epistemological reading • The ontological reading ifomis.org

17. 1) The linguistic reading • A concept is a meaning that is shared in common by a collection of synonymous terms ifomis.org

18. Unified Medical Language System • is_a =def. • If one item ‘is_a’ another item then the first item is more specific in meaning than the second item. ifomis.org

19. Fruit similarTo Vegetable Orange Apfelsine synonymWith NarrowerTerm Semantic Networks Goble & Shadbolt ifomis.org

20. The linguistic reading is bad • for work on ontologies in support of research in the natural sciences / evidence-based medicine ifomis.org

21. Problem of evaluation • a good ontology/terminology/vocabulary = one which corresponds to reality as it exists beyond our concepts • if an ontology is a mere network of meanings, then the distinction between good and bad ontologies loses its foothold ifomis.org

22. angel or devil are perfectly good concepts • so are • cancelled performance • avoided meeting • prevented pregnancy • imagined mammal • alien implant removal • Chios energy healing ifomis.org

23. The linguistic reading • yields a more or less coherent reading of relations like: • ‘is_a’ • ‘synonymous_with’ • ‘associated_to’ • but it fails miserably when it comes to relations of other types ifomis.org

24. part_of • heart part_of human • human heart part_of human • testis part_of human • human testis part_of human • but not: human has_part human testis ifomis.org

25. how can concepts, on the linguistic reading, figure as relata of relations like: • part_of = def. composes, with one or more other physical units, some larger whole • contains =def. is the receptacle for fluids or other substances ifomis.org

26. How can a set of synonymous terms serve as • a receptacle for fluids or other substances? ifomis.org

27. The psychological reading of ‘concept’ Concepts are ideas in the minds of human subjects ifomis.org

28. Eugen Wüster • 1935 • Professor of • Woodworking • Machinery • in the Vienna • Agricultural • College ifomis.org

29. Eugen Wüster • Terminology- • hobbyist • and • founder of • International • Standards • Organization • Technical • Committee 37 ifomis.org

30. International Standard Bad Philosophy • Wüster: concepts are inside people’s brains •  ISO terminology standards ifomis.org

31. Wüster • a concept is a mental surrogate of a plurality of objects grouped together on the basis of perceived similarities • and what makes those objects similar is another concept • (Turtles all the way down) ifomis.org

32. ISO: Terminologists should still postulate ‘concepts’ even when they have no idea of what the terms in question mean • In the domain of woodworking equipment we can seethe similarities between groups of objects to which general terms are assigned. • Not so in medicine (consider: a carcinoma, or an embryo, in the successive phases of its development) ifomis.org

33. Wüster / ISO on ‘objects’ • object = def. anything to which human thought is or can be directed • ... whether material or immaterial, real or purely imagined • ISO:In the course of producing a terminology, philosophical discussionson whether an object actually exists in reality … are to be avoided. ifomis.org

34. 3) The epistemological reading • Concepts are ‘units of knowledge’ • as in ‘knowledge modeling’, ‘knowledge representation’, ‘knowledge-intense disciplines’ • Even errors are ‘knowledge’ on this reading • – so here, too, the concept orientation draws as too far away from empirical science and too close to delusion and myth ifomis.org

35. Against ‘knowledge representation’ • Not • ‘KNOWLEDGE-BASED SYSTEMS’ • but • ‘true-or-false-belief-based systems’ ifomis.org

36. Concepts are Triply Ethereal • because they are simultaneously supposed to be • software proxies for entities in reality • (some ghostly diabetes counterpart is needed – because “you can’t get the diabetes itself inside the computer”) • 2. the ‘knowledge’ (ideas and beliefs) in the minds of human experts • 3. the meanings of the terms such experts use ifomis.org

37. ifomis.org

38. 4) The ontological reading • concepts are not creatures of cognition or of computation • they are invariants out there in reality • Better: they are what philosophers call types, kinds, universals ifomis.org

39. is_a • human is_a mammal • all instances of the universal human are instances of the universal mammal • is_a defined in terms of the primitive relation of instantiation between a particular and a universal ifomis.org

40. part_of • defined in terms of the primitive relation of mereological parthood defined between one instance and another (for example between Mary and her heart) • A part_of B =def. given any instance a of A there is some instance b of B such that a part_of b ifomis.org

41. inverse relations • nucleus part_of cell • cell has_part nucleus ifomis.org

42. All-some definitions of relations between universals • A adjacent_to B =def • all instances of A are adjacent to (in the instance-level sense) some instance of B ifomis.org

43. Ajacency as a relation between universals is not symmetrical • nucleus adjacent_to cytoplasm • Not: cytoplasm adjacent_to nucleus • seminal vesicle adjacent_to urinary bladder • Not: urinary bladderadjacent_to seminal vesicle ifomis.org

44. Evaluation • Bad ontologies are (inter alia) those whose general terms lack the relation to corresponding universals in reality, and thereby also to corresponding instances. ifomis.org

45. Good ontologies • = representations of universals and particulars in reality ifomis.org

46. The concept diabetes mellitus becomes ‘associated with a diabetic patient’ • concept patient concept diabetes • what it is on the • side of the patient ? ? ifomis.org

47. what is the relation here? The concept diabetes mellitus becomes ‘associated with a diabetic patient’ • concept patient concept diabetes • what it is on the • side of the patient ? ? ifomis.org

48. Make this our starting point • what it is on the • side of the patient + substance accident ifomis.org

49. A bottom-up approach • begin with what confronts the physician at the point of care (or in the lab): • instances in reality (patients, disorders, pains, fractures, ...) • = the what it is on the side of the patient • and build up to terminologies from there ifomis.org

50. What happens when a new disorder first begins to make itself manifest? • physicians delineate a certain family of cases manifesting a new pattern of symptoms • ... hypothesis: they are instances of a single universal or kind • (this universal still hardly understood) • but already: need for a new term (e.g. ‘AIDS’) ifomis.org