Werner CEUSTERS, MD Center of Excellence in Bioinformatics and Life Sciences

1. “Ontology Measurement and evaluation" mini-seriesRealism-based Change Management for Quality Assurance in Ontologies and Data RepositoriesNIST-Ontolog-NCOR, Januari 11, 2007 Werner CEUSTERS, MD Center of Excellence in Bioinformatics and Life Sciences Department of Psychiatry, University at Buffalo, NY, USA http://www.org.buffalo.edu/RTU

2. Outline • A realist view on ontology • Coping with changes • Tracking changes in ontologies and repositories • A calculus for quality assurance of updates

3. Part 1: A Realist View on Ontology

4. An unfortunate perception of ‘ontology’ • The most widespread view of what an ontology is, is that of ‘an explicit specification of the conceptualization of a domain’ (Gruber), • often complemented with the notion of ‘agreement’.

5. This view on ontology has sad consequences • Too much effort goes into the specification business • OWL, DL-reasoners, translators and convertors, syntax checkers, ... • Too little effort into the faithfulness of the conceptualizations towards what they represent. • Pseudo-separation of language and entities • “absent nipple” • Many ‘ontologies’ and ontology-like systems exhibit mistakes of various sorts.

6. The remedy: a realist view of the world • The world consists of • entities that are • Either particulars or universals; • Either occurrents or continuants; • Either dependent or independent; and, • relationships between these entities of the form • <particular , universal> e.g. is-instance-of, • <particular , particular> e.g. is-member-of • <universal , universal> e.g. isa (is-subtype-of) 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, November 8, 2006, Baltimore MD, USA

7. Three levels of reality • The world exists ‘as it is’ prior to a cognitive agent’s perception thereof; 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, November 8, 2006, Baltimore MD, USA

8. R Reality exist before any observation

9. R And also most structures in reality are there in advance. Reality exist before any observation

10. Three levels of reality • The world exists ‘as it is’ prior to a cognitive agent’s perception thereof; • Cognitive agents build up ‘in their minds’ cognitive representations of the world; 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, November 8, 2006, Baltimore MD, USA

11. The ontology author acknowledges the existence of some Portion Of Reality (POR) B R

12. B Some portions of reality escape his attention. R

13. Three levels of reality • The world exists ‘as it is’ prior to a cognitive agent’s perception thereof; • Cognitive agents build up ‘in their minds’ cognitive representations of the world; • To make these representations publicly accessible in some enduring fashion, they create representational artifacts that are fixed in some medium. 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, November 8, 2006, Baltimore MD, USA

14. He represents only what he considers relevant B RU1B1 • Both RU1B1 and RU1O1 are representational units referring to #1; • RU1O1 is NOT a representation of RU1B1; • RU1O1 is created through concretization of RU1B1 in some medium. RU1O1 O #1 R

15. We should not be in the business of “concept representation” Thus ... • These concretizations are NOT supposed to be the representations of these cognitive representations;

16. But beware ! • These concretizations are NOT supposed to be the representations of these cognitive representations; • They are representations of the corresponding parts of reality • They are like the images taken by means of a high quality camera;

17. They are not(or should not be) like the paintings of Salvador Dali Non-canonical (although nice looking) anatomy

18. Representational artifacts • Ideally built out of representational units and relationships that mirror the entities and their relationships in reality.

19. Some characteristics of representational units • each unit is assumed by the creators of the representation to be veridical, i.e. to conform to some relevant POR as conceived on the best current scientific understanding;

20. Some characteristics of representational units • each unit is assumed by the creators of the representation to be veridical, i.e. to conform to some relevant POR as conceived on the best current scientific understanding; • several units may correspond to the same POR by presenting different though still veridical views or perspectives;

21. Some characteristics of representational units • each unit is assumed by the creators of the representation to be veridical, i.e. to conform to some relevant POR as conceived on the best current scientific understanding; • several units may correspond to the same POR by presenting different though still veridical views or perspectives; • what is to be represented by the units in a representation depends on the purposes which the representation is designed to serve.

22. Some characteristics of an optimal ontology • Each representational unit in such an ontology would designate • (1) a single portion of reality (POR), which is • (2) relevant to the purposes of the ontology and such that • (3) the authors of the ontology intended to use this unit to designate this POR, and • (4) there would be no PORs objectively relevant to these purposes that are not referred to in the ontology.

23. But things may go wrong … • assertion errors: ontology developers may be in error as to what is the case in their target domain;

24. B O R Assertion error RU1B1 RU1O1 #1

25. But things may go wrong … • assertion errors: ontology developers may be in error as to what is the case in their target domain; • relevance errors: they may be in error as to what is objectively relevant to a given purpose;

26. B O R Relevancy error RU1B1 RU1O1 #1

27. But things may go wrong … • assertion errors: ontology developers may be in error as to what is the case in their target domain; • relevance errors: they may be in error as to what is objectively relevant to a given purpose; • encoding errors: they may not successfully encode their underlying cognitive representations, so that particular representational units fail to point to the intended PORs.

28. B O R Encoding error RU1B1 RU1O1 #1

29. Example: medical ‘findings’ and ‘observations’ (1) • A particular pathological entity may at a certain time be undetectable by any observation method or technique available to an observer, including the person exhibiting the pathological entity itself.

30. Example: medical ‘findings’ and ‘observations’ (1) • A particular pathological entity may at a certain time be undetectable by any observation method or technique available to an observer, including the person exhibiting the pathological entity itself. • A particular observation may produce false results and thus simulate the existence of a pathological entity.

31. Example: medical ‘findings’ and ‘observations’ (1) • A particular pathological entity may at a certain time be undetectable by any observation method or technique available to an observer, including the person exhibiting the pathological entity itself. • A particular observation may produce false results and thus simulate the existence of a pathological entity. • An observer may observe or fail to observe a detectable particular pathological entity.

32. On ‘findings’ and ‘observations’ (2) • When an observer perceives a particular pathological entity, he might judge it • (1) to be an instance of the universal of which it is indeed an instance in reality, • (2) to be an instance of another universal (and thus be in error), or • (3) he might be not able to make an association with any universal at all. • Distinct manifestations of ‘the same type’ may be pathological or not: • Singing naked under the shower versus in front of The White House • ...

33. Part 2:Coping with changes

34. t U1 U2 Reality p3 Reality versus beliefs, both in evolution

35. t U1 U2 Reality p3 Reality versus beliefs, both in evolution IUI-#3 O-#0 O-#2 Belief O-#1 = “denotes” = what constitutes the meaning of representational units …. Therefore: O-#0 is meaningless

36. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 Total ignorance: e.g. a disease (U1) already exist but we have no clue about it

37. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 False belief in the existence of a type, e.g. ‘unicorn’, ‘diabolic possession’ Note: happens also at the level of particulars: e.g. the planet ‘Vulcan’

38. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 The coming into existence of a new universal remains unnoticed: e.g. ‘AIDS’ existed before being discovered.

39. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 The coming into being of a new particular remains unnoticed: e.g. John Doe’s colonic polyp, which from that time on, is an instance of U1.

40. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 An advance in science: the existence of U1 is acknowledged.

41. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 The existence of John Doe’s benign colonic polyp is discovered, however, without being recognized as such. Rather, it is believed to be an instance of what in reality is a fantasy.

42. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 Another advance in science: the ‘concept’ O-#0 is rightfully abandoned, necessitating therefor to reconsider of what p3 must be believed to be an instance of.

43. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 It is, rightfully believed that p3 is an instance of U1. It raises, amongst other things, the question to what point in history this belief can be extended.

44. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 p3 changes from a benign into a malignant tumor, at a time that science did not discover malignancy yet. p3 is now wrongly believed to be an instance of U1.

45. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 Advance in science: “malignancy” is discovered. However, that it applies to John Doe’s polyp has not yet been noticed.

46. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 John Doe’s polyp becomes recognized as an instance of a malignant tumor.

47. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 John Doe’s polyp was irradiated and believed to have vanished, while in reality, it isn’t.

48. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 John Doe is lucky: his tumor indeed disappeared. His physicians who believed it was already gone, are lucky also: they escape a law suite.

49. Reality versus beliefs, both in evolution t U1 U2 R p3 IUI-#3 O-#0 O-#2 B O-#1 For ‘utilitarian’ reasons, the “pragmatic engineers” remove malignant tumors from their ontology: if it is not believed to exist, you can’t get law suites for failures in recognizing instances.

50. Some other possible situations t U1 U2 R p3 IUI-#3 IUI-#3 O-#0 O-#2 B O-#1 A particular is believed to exist longer than it really does. e.g. “Elvis is not dead”, or the innumerous EHRs that state the patient taking some drug while he stopped.