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

1. Discovery Seminar 118330/UE 141 CC – Fall 2007Difficult Problems, Easy Solutions: Referent Tracking in BiomedicineSession: 10/08/2007A detailed account of realism-based ontologies 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. Presentation overview • ‘Traditional’ ontology approaches and associated problems • Realism-based ontology: • Fundamental principles • Basic entities: particulars and universals • Relationships • Ontology evolution

3. Concept-based ontologies

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. Central in this view are ‘concepts’ • But what the word ‘concept’ denotes, is never clarified and users of it often refer to different entities in a haphazard way: • meaning shared in common by synonymous terms • idea shared in common in the minds of those who use these terms • unit of describing meanings knowledge • universal that what is shared by all and only all entities in reality of a similar sort 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

6. Central in this view are ‘concepts’ • But what the word ‘concept’ denotes, is never clarified and users of it often refer to different entities in a haphazard way: • meaning shared in common by synonymous terms • idea shared in common in the minds of those who use these terms • unit of describing meanings knowledge • universal that what is shared by all and only all entities in reality of a similar sort These views require the involvement of a cognitive entity:

7. Central in this view are ‘concepts’ • But what the word ‘concept’ denotes, is never clarified and users of it often refer to different entities in a haphazard way: • meaning shared in common by synonymous terms • idea shared in common in the minds of those who use these terms • unit of describing meanings knowledge • universal that what is shared by all and only all entities in reality of a similar sort These views require the involvement of a cognitive entity: This view does not presuppose cognition at all

8. Concept-orientation in 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.

9. Realism-based ontology:reality comes first,representation is second.

10. Ontologies as representations of reality • A taxonomy: is a tree-form graph-theoretic representational artifact with nodes representing universals or classes and edges representing isa or subset relations. • An ontology: is a representational artifact, comprising a taxonomy as proper part, whose representational units are intended to designate some combination of universals, defined classes, and certain relations between them. • A realism-based ontology: is built out of representational units which are intended to refer exclusively to universals, and corresponds to that part of the content of a scientific theory that is captured by its constituent general terms and their interrelations. 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

11. 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

12. R Reality exist before any observation

13. R And also most structures in reality are there in advance. Reality exist before any observation • Humans had a brain well before they knew they had one. • Trees were green before humans started to use the word “green”.

14. 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

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

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

17. 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

18. 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

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

20. 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.

21. Basic components of 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, lacks • <particular , particular> e.g. is-member-of, is-part-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

22. The example to work (partially) out: ‘walking’ process living creature function Is_a Is_a leg Is_a Instance-of at t humanbeing legmoving walking Instance-of at t Instance-of Instance-of at t to make me walk this leg moving Has-function at t Has- Participant at t Instance-of part-of at t part-of my left leg Is-realized- In at t me this walking Has-participant at t2

23. Basic entities inrealism-based ontology:three main distinctions 1 2 3

24. to make me walk this leg moving my left leg me this walking Particulars 1 Individual entities that carry identity and preserve their identity over time

25. process living creature function leg humanbeing legmoving walking Universals 1 Entities which exist “in” the particulars amongst which there is a relation of similarity not found with other particulars

26. process living creature function leg Instance-of at t humanbeing legmoving walking Instance-of at t Instance-of Instance-of at t to make me walk this leg moving Instance-of my left leg me this walking Particulars and Universals 1

27. process living creature function leg Instance-of at t humanbeing legmoving walking Instance-of at t Instance-of Instance-of at t to make me walk this leg moving Instance-of my left leg me this walking Continuants and Occurrents 2

28. Continuants 2 Continuants are entities which endure (=continue to exist) while undergoing different sorts of changes, including changes of place. While they exist, they exist “in total”. function leg Instance-of at t humanbeing Instance-of at t Instance-of at t to make me walk my left leg me

29. Preserving identity through change 2 human being t me me child adult Instance-of in 1960 Instance-of since 1980 living creature animal caterpillar butterfly

30. Occurrents 2 Occurrents are changes. Occurrents unfold themselves during temporal phases. At any point in time, they exist only in part. legmoving walking Instance-of this leg moving Instance-of this walking

31. Independent versus dependent 3 process living creature function Is_a Is_a leg Is_a Instance-of at t humanbeing legmoving walking Instance-of at t Instance-of Instance-of at t to make me walk this leg moving Instance-of my left leg me this walking

32. Independent entities Do not require any other entity to exist to enable their own existence Dependent entities Require the existence of another entity for their existence Independent versus dependent 3 to make me walk this leg moving my left leg me this walking

33. Independent entities Do not require any other entity to exist to enable their own existence Dependent entities Require the existence of another entity for their existence Independent versus dependent 3 to make me walk this leg moving Independent continuants Dependent continuants Occurrents (are all dependent) my left leg me this walking

34. Dependent continuants 3 • Realized • Quality: redness (of blood) • Realizable • Function: to flex (of knee joint) • Role: student • Power: boss • Disposition: brittleness (of a bone)

35. continuants occurrents Realizations flexing studying ordering breaking Dependent continuants 3 • Realized • Quality: redness (of blood) • Realizable • Function: to flex (of knee joint) • Role: student • Power: boss • Disposition: brittleness (of a bone)

36. Relationsinrealism-based ontology Smith B, Ceusters W, Klagges B, Koehler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector A, Rosse C. Relations in biomedical ontologies, Genome Biology 2005, 6:R46.

37. ? Basic sorts of relationships universal universal particular particular

38. extention-of Defined class member-of Universals and classes universal instance-of P P P P P P P P P P P P

39. General principle about relationships All universal level relationships are defined on the basis of particular level relationships

40. Primitive instance-level relationships • c instance_of C at t- a primitive relation between a continuant instance and a class which it instantiates at a specific time • p instance_of P- a primitive relation between a process instance and a class which it instantiates holding independently of time • c part_of c1 at t- a primitive relation between two continuant instances and a time at which the one is part of the other • p part_of p1, r part_of r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other) • c located_in r at t- a primitive relation between a continuant instance, a spatial region which it occupies, and a time • r adjacent_to r1 - a primitive relation of proximity between two disjoint continuants • t earlier t1 - a primitive relation between two times • c derives_from c1 - a primitive relation involving two distinct material continuants c and c1 • p has_participant c at t- a primitive relation between a process, a continuant, and a time • p has_agent c at t- a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process

41. Is_a is defined over instance-of (1) For continuants • C is_a C1 = [definition] for allc, t, if c instance_of C at t then c instance_of C1 at t. For occurrents • P is_a P1 = [definition] for allp, if p instance_of P then p instance_of P1.

42. is_a instance-of at t Is_a is defined over instance-of (2) universals living creature human being me particulars

43. Is_a is defined over instance-of (3) More than subset or inclusion ! living creature is_a human being animal is_a is_a child adult caterpillar butterfly Instance-of t1 t2 me

44. Transformation Derivation continuation fusion fission

45. part-of at t part-of Part-of different for continuants and occurrents process living creature Is_a Is_a leg Is_a humanbeing legmoving walking Instance-of at t Instance-of Instance-of at t this leg moving Instance-of my left leg me this walking

46. part-of at t Part-of can be generalized, … with care ! C part_of C1 = [def] for all c, t, if Cct then there is some c1 such that C1c1t and c part_of c1 at t. living creature leg Is_a humanbeing Instance-of at t Instance-of at t my left leg me Cct = c instance-of C at t

47. ? Part-of part-of at t Part-of can be generalized, … with care ! C part_of C1 = [def] for all c, t, if Cct then there is some c1 such that C1c1t and c part_of c1 at t. living creature leg Is_a humanbeing Instance-of at t Instance-of at t my left leg me Cct = c instance-of C at t

48. ? Part-of part-of at t Part-of can be generalized, … with care ! • Horse legs are not parts of human beings • Amputated legs are not parts of human beings • ‘Canonical leg is part of canonical human being’, but…, there are (very likely) no such particulars • … living creature leg Is_a humanbeing Instance-of at t Instance-of at t my left leg me

49. part-of Generalization of temporal parthood • P part_of P1 = [definition] • for all p, • if Pp • then there is some p1 such that: P1p1 and p part_of p1 process Is_a Is_a legmoving walking Instance-of this leg moving Instance-of this walking

50. Two sorts of temporal parthood (1) • ‘longitudinal’: one process evolves as part of another one. • May involve stronger relationships of other types, e.g. causal process Is_a Is_a legmoving walking Instance-of this leg moving Has- Participant at t Instance-of part-of at t part-of my left leg me this walking Has-participant at t2