1. 1 Basic Formal Ontology Barry Smith http://ontologist.com March 2004 http://ontologist.com

2. 2

3. 3 The problem Different communities of medical researchers use different and often incompatible category systems in expressing the results of their work

4. 4 The solution “ONTOLOGY” Remove “Ontology Impedance” But what does “ontology” mean?

5. 5 Two alternative readings Ontologies are oriented around terms or concepts = currently popular IT conception Ontologies are oriented around the entities in reality = traditional philosophical conception, embraced also by IFOMIS

6. 6 Ontology as a branch of philosophy seeks to establish the science of the kinds and structures of objects, properties, events, processes and relations in every domain of reality

7. 7 Ontology a kind of generalized chemistry or zoology (Aristotle’s ontology grew out of biological classification)

8. 8 Aristotle world’s first ontologist

9. 9 World‘s first ontology ( from Porphyry’s Commentary on Aristotle’s Categories)

10. 10 Linnaean Ontology

11. 11 Ontology is distinguished from the special sciences it seeks to study all of the various types of entities existing at all levels of granularity

12. 12 and to establish how they hang together to form a single whole (‘reality’ or ‘being’)

13. 13 different concept/terminology systems

14. 14 need not interconnect at all for example they may relate to entities of different granularity

15. 15 we cannot make incompatible terminology-systems interconnect just by looking at concepts, or knowledge or language

16. 16 we cannot make incompatible terminology-systems interconnect by staring at the terminology systems themselves

17. 17 to decide which of a plurality of competing definitions to accept we need some tertium quid

18. 18 we need, in other words, to take the world itself into account

19. 19 BFO = basic formal ontology

20. 20 BFO ontology is defined not as the ‘standardization’ or ‘specification’ of conceptualizations (not as a branch of knowledge or concept engineering) but as an inventory of the entities existing in reality

21. 21 The BFO framework will solve the problem of ontological impedance and provide tools for quality-control on the output of computer applications

22. 22 BFO not a computer application but a Reference Ontology (something like old-fashioned metaphysics)

23. 23 Reference Ontology a theory of a domain of entities in the world

24. 24 BFO not just a system of categories but a formal theory with definitions, axioms, theorems designed to provide the resources for reference ontologies for specific domains of sufficient richness that terminological incompatibilities can be resolved intelligently rather than by brute force

25. 25 Proposed solution distinguish two separate tasks: - the task of developing computer applications capable of running in real time -the task of developing an expressively rich framework of a sort which will allow us to resolve incompatibilities between definitions and formulate intuitive and reliable principles for database curation

26. 26 Reference Ontology a theory of the tertium quid – called reality – needed to hand-callibrate database/terminology systems

27. 27 Methodology Get ontology right first (realism; descriptive adequacy; rather powerful logic); solve tractability problems later

28. 28

29. 29 Realist Perspectivalism There is a multiplicity of ontological perspectives on reality, all equally veridical i.e. transparent to reality

30. 30 Anatomy vs. Pathology

31. 31 The Problem The tumor developed in John’s lung over 25 years

32. 32 The Problem ____ developed in _____ over 25 years process state

33. 33 The Problem The tumor developed in the lung over 25 years substances things objects continuants

34. 34 The Problem The tumor developed in John’s lung over 25 years PARTHOOD NOT DETERMINATE

35. 35 The Problem The tumor developed in the lung over 25 years substances GLUING THESE TOGETHER YIELDS ONTOLOGICAL MONSTERS processes

36. 36 Substances and processes exist in time in different ways substance t i m e process

37. 37 SNAP vs SPAN Endurants vs perdurants Continuants vs occurrents In preparing an inventory of reality we keep track of these two different kinds of entities in two different ways

38. 38 No way in which sums of substances and processes can exist in time … hence

39. 39 Fourdimensionalism – only processes exist – time is just another dimension, analogous to the three spatial dimensions – substances are analyzed away as worms/fibers within the four- dimensional plenum

40. 40 There are no substances Bill Clinton does not exist Rather: there exists within the four- dimensional plenum a continuous succession of processes which are similar in a Billclintonizing way

41. 41 Fourdimensionalism (the SPAN perspective) is right in everything it says But incomplete

42. 42 Realist Perspectivalism There is a multiplicity of ontological perspectives on reality, all equally veridical = transparent to reality

43. 43 Need for different perspectives Not one ontology, but a multiplicity of complementary ontologies Cf. particle vs. wave ontologies in quantum mechanics

44. 44 Two Orthogonal, Complementary Perspectives SNAP and SPAN

45. 45 Snapshot Video ontology ontology substance t i m e process

46. 46 SNAP and SPAN stocks and flows commodities and services product and process anatomy and physiology

47. 47 SNAP and SPAN SNAP entities - have continuous existence in time - preserve their identity through change - exist in toto if they exist at all SPAN entities - have temporal parts - unfold themselves phase by phase - exist only in their phases/stages

48. 48 You are a substance Your life is a process You are 3-dimensional Your life is 4-dimensional

49. 49 Many SNAP Ontologies t1t1 t3t3 t2t2 here time exists outside the ontology, as an index or time-stamp

50. 50 each SNAP i section through reality includes everything which exists (present tense)

51. 51 mereology works without restriction (parthood is everywhere determinate) in every SNAP i ontology

52. 52 Three kinds of SNAP entities 1.Substances (Independent) 2.SNAP Dependent Entities 3.Spatial regions, contexts, niches, environments

53. 53 SNAP dependent entities States, powers, qualities, roles … functions, dispositions, plans, shapes, status, habitus, liabilities … = dependent SNAP entities

54. 54 SNAP dependent entities: one-place: your temperature, color, height my knowledge of French the whiteness of this cheese the warmth of this stone the fragility of this glass

55. 55 relational SNAP dependent entities John Mary love stand in relations of one-sided dependence to a plurality of substances simultaneously specific dependence

56. 56 Three kinds of SNAP entities 1.Substances 2.Dependents 3.Spatial regions, contexts, niches, environments

57. 57 Spatial regions + sites (contexts, niches, environments) Organism species evolve into environments Domesticated spatial regions: rooms, nostrils, your alimentary tract Fiat spatial regions: JFK designated airspace

58. 58

59. 59 SNAP: Entities existing in toto at a time

60. 60 The SPAN Ontology t i m e

61. 61 here time exists as part of the domain of the ontology The SPAN ontology

62. 62 mereology works without restriction everywhere here t i m e clinical trial

63. 63 Processes, too, are dependent on substances One-place vs. relational processes One-place processes: your getting warmer your getting hungrier

64. 64 Examples of relational processes kissings, thumpings, conversations, dancings, join their carriers together into collectives of greater or lesser duration

65. 65 SPAN: Entities extended in time

66. 66 Relations to DOLCE SNAP vs. SPAN One ontology or many? Qualities are SNAP entities Treatment of space as quality Quality regions (temperature, color, height)

67. 67 Two kinds of SPAN entities 1.Processes (including events: process-boundaries, settings) 2.Spatio-temporal regions

68. 68 Settings = 4-dimensional environments Lobsters have evolved into environments marked by cyclical patterns of temperature change Tudor England The Afghan winter The window of opportunity for an invasion of Iraq

69. 69 How do you know whether an entity is SNAP or SPAN?

70. 70 problem cases forest fire anthrax epidemic hurricane Maria traffic jam ocean wave

71. 71 forest fire: a process a pack of monkeys jumping from tree to tree and eating up the trees as they go the Olympic flame: a process or a thing? (anthrax spores are little monkeys)

72. 72 The Epidemic (SNAP) The Spread of an Epidemic (SPAN)

73. 73 Material examples: performance of a symphony projection of a film expression of an emotion utterance of a sentence application of a therapy course of a disease increase of temperature

74. 74 The Gene Ontology is so confused about ‘functions’ and ‘processes’ because it does not have the distinction between SNAP and SPAN (between function and functioning)

75. 75 How link SNAP and SPAN together? via formal relations = entities which do not add anything to being

76. 76 Successive Causality SNAP-SPAN: Agent causation A substance produces causally a process SPAN-SPAN: Process causation One process causes another process SPAN-SNAP: Causal repercussion A process results in the modification of a substance (always mediated by process causation) SNAP-SNAP: Causal origin One substance is the causal origin of another (mediated by other types of causal relations )

77. 77 Successive Causality SNAP-SPAN: Agent causation SPAN-SPAN: Process causation SPAN-SNAP: Causal repercussion SNAP-SNAP: Causal origin

78. 78 Simultaneous causality SPAN-SPAN The rise in temperature causes the (simultaneous) increase in pressure (Boyle’s law)

79. 79 Substance  Process PARTICIPATION (a species of dependence)

80. 80 Participation (SNAP-SPAN) A substance (SNAP) participates in a process (SPAN) A runner participates in a race A voter participates in an election

81. 81 Axes of variation activity/passivity (agentive) direct/mediated benefactor/malefactor (conducive to existence) [MEDICINE]

82. 82 SNAP-SPAN Participation Perpetration (+agentive) Initiation Perpetuation Termination Influence Facilitation Hindrance Mediation Patiency (-agentive)

83. 83 Perpetration A substance perpetrates an action (direct and agentive participation in a process): The referee fires the starting-pistol The captain gives the order

84. 84 Initiation A substance initiates a process: The referee starts the race The attorney initiates the process of appeal

85. 85 Perpetuation A substance sustains a process: The singer sings the song The charged filament perpetuates the emission of light

86. 86 Termination A substance terminates a process: The operator terminates the projection of the film The judge terminates the imprisonment of the pardoned convict

87. 87 Influence A substance (or its quality) has an effect on a process The steepness of the slope affects the movement of the troops The politicians influence the course of the war

88. 88 Hindrance, prevention A substance has a negative effect on the unfolding of a process (by participating in other processes) The drug hinders the progression of the disease The strikers prevent the airplane from departing

89. 89 Mediation A substance plays an indirect role in the unfolding of a process relating other participants: The Norwegians mediate the discussions between the warring parties

90. 90 Patiency Dual of agentive participation John kisses [Mary] (John agent) Mary is kissed [by John] (Mary patient)

91. 91 Signatures of meta-relations SNAP ComponentSPAN Component Substances SPQR… Space Regions Processuals Processes Events Space-Time Regions

92. 92 Signatures of meta-relations SNAP ComponentSPAN Component Substances SPQR… Space Regions Processuals Processes Events Space-Time Regions

93. 93 Signatures of meta-relations SNAP ComponentSPAN Component Substances SPQR… Space Regions Processuals Processes Events Space-Time Regions

94. 94 Signatures of meta-relations SNAP ComponentSPAN Component Substances SPQR… Space Regions Processuals Processes Events Space-Time Regions

95. 95 REALIZATION

96. 96 Signatures of meta-relations SNAP ComponentSPAN Component Substances SPQR… Spatial Regions Processuals Processes Events Space-Time Regions participation realization

97. 97 Realization (SPQR  process) The most general relation between a dependent (SPQR…) entity and a process The power to legislate is realized through the passing of a law The role of antibiotics in treating infections is via the killing of bacteria

98. 98 Realization (SNAP-SPAN) the execution of a plan, algorithm the expression of a function the exercise of a role the realization of a disposition

99. 99 SPQR… entities and their SPAN realizations plan function role disposition algorithm SNAP

100. 100 SPQR… entities and their SPAN realizations execution expression exercise realization application course SPAN

101. 101 SNAP  SPAN Participation Substance  Process Realization SPQR  Process

102. 102 Creation A process brings into being a substance: The declaration of independence creates the new state The work of the potter creates the vase

103. 103 Sustaining in being A process sustains in being a substance: The circulation of the blood sustains the body Levying taxes sustains the army

104. 104 Degradation A process has negative effects upon a substance Eating sugar contributes to the deterioration of your teeth. The flow of water erodes the rock

105. 105 Destruction A process puts a substance out of existence The explosion destroys the car The falling of the vase on the floor breaks it

106. 106 Demarcation A process creates (fiat or bona fide) boundaries of substances. The signing of the treaty establishes fixed borders between the two nations The tracing of the area of operation by the surgeon defines a boundary, the incision performed by the surgeon yet another one

107. 107 Blurring A process destroys boundaries of substances: The military stand-off creates the no man's land The successful transplant obliterates the boundary between original and grafted tissue

108. 108 Creation A process brings into being a dependent SNAP entity (quality, shape) The accident reshapes the car. The baking of the clay gives the vase its rigidity and color.

109. 109 Continuation A process sustains the existence of a dependent SNAP entity The firing of the fireworks maintains the coloration of the sky The intake of alcohol sustains the rosiness of his cheeks

110. 110 Destruction A process destroys/changes a dependent SNAP entity The accident destroys the car's shape The burning of the vase destroys its color The demotion relieved him of his rank as an officer

111. 111 SNAP-SPAN Participation Perpetration (+agentive) Initiation Perpetuation Termination Influence Facilitation Hindrance Mediation Patiency (-agentive)

112. 112 SPAN-SNAP Involvement Creation Sustenance Destruction Continuation Degradation Destruction Creation Demarcation Blurring Qualitative projection Degradation

113. 113 Realist Perspectivalism There is a multiplicity of ontological perspectives on reality, all equally veridical i.e. transparent to reality

114. 114 Cardinal Perspectives SNAP vs. SPAN Granularity (Micro vs. Meso vs. Macro)

115. 115 Cardinal Perspectives SNAP vs. SPAN Granularity (Micro vs. Meso vs. Macro)

116. 116 Ontological Zooming

117. 117 Ontological Zooming human anatomy cellular anatomy

118. 118 Part-Whole Basic relation exclusively intra- ontological: either SNAP-SNAP or SPAN-SPAN. SNAP-SNAP: only if SNAP i s have the same temporal index

119. 119 Relations crossing the SNAP/SPAN border are never part-relations John’s life substance John physiological processes sustaining in existence

120. 120 Granularity spatial regionsubstance parts of substances are always substances

121. 121 Granularity spatial regionsubstance parts of spatial regions are always spatial regions

122. 122 Granularity process parts of processes are always processes

123. 123 Intra-granular and cross-granular parthood across SNAPs: Kevin’s arm is part of Kevin Kevin’s molecule is part of Kevin across SPANs: Kevin’s leg-movement is part of Kevin’s running Kevin’s cytometabolism is part of Kevin’s running

124. 124 THE END