1 BFO and GOL Ontological theory vs. ontology language GOL as an ontology representation language analogous to KIF (thus maximally eclectic) BFO as an ontological theory of reality designed as a real constraint on domain ontologies

2 A Network of Domain Ontologies Material (Regional) Ontologies Basic Formal Ontology

3 A Network of Domain Ontologies BFO

4 A Network of Domain Ontologies BFO ChemO

5 A Network of Domain Ontologies BFO ChemOMedO

6 Nouns and verbs Substances and processes Continuants and occurrents In preparing an inventory of reality we keep track of these two different categories of entities in two different ways

7 Natural language glues them together indiscriminately substance t i m e process

8 Snapshot vs. Video substance t i m e process

9 Substances Mesoscopic reality is divided at its natural joints into substances: animals, bones, rocks, potatoes

10 The Ontology of Substances Substances form natural kinds (universals, species + genera)

11 Not only substances exist in toto at any time at which they exist at all the same holds of qualities, and of roles, functions, powers, dispositions – each of these has executions (processes)

12 Processes t i m e

13 Processes Processes merge into one another Process kinds merge into one another … few clean joints either between instances or between types

14 Some clean joints derive from the fact that processes are dependent on substances (my headache is cleanly demarcated from your headache)

15 Some clean joints in realms of artefactual processes: weddings chess games dog shows ontology tutorials sharp divisions imputed via clocks, calendars

16 Clean joints also through language = fiat demarcations Quinean gerrymandering ontologies are attractive for processes not for substances Quine: there are no substances

17 Substances and processes t i m e process demand different sorts of inventories

18 Substances demand 3-D partonomies space

19 Processes demand 4D-partonomies t i m e

20 Processes have temporal parts The first 5 minutes of my headache is a temporal part of my headache The first game of the match is a temporal part of the whole match

21 Substances do not have temporal parts The first 5-minute phase of my existence is not a temporal part of me It is a temporal part of that complex process which is my life

22 Qualities, Roles, Functions, Powers, Dispositions Do not have temporal parts They belong to the SNAP ontology

23 How do we glue these two different sorts of entities together mereologically? How do we include them both in a single inventory of reality

24 How do we fit these two entities together within a single system of representations? within a directly depicting language?

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

26 Substances and processes form two distinct orders of being Substances exist as a whole at every point in time at which they exist at all Processes unfold through time, and are never present in full at any given instant during which they exist. When do both exist to be inventoried together?

27 1. Four-dimensionalism All entities are spatio-temporally extended portions of an atemporal four-dimensional whole called reality Problems: substances (e.g. people) do not exist change does not exist

28 2. Presentism Both substances and processes exist, but only what exists now exists at all. Problem: ‘Napoleon ruled before Clinton’

29 Neither of these solutions is completely adequate Hence a good formal ontology must somehow contain them both

30 A good formal ontology must divide into two sub-ontologies: 1. a four-dimensionalist ontology (of processes) SPAN cf. Quine 2. a modified presentist ontology cf. Brentano, Aristotle, Chisholm (takes tense seriously) SNAP

31 These represent two views of the same rich and messy reality, the reality captured promiscuously by TEE

32 The SPAN Ontology t i m e

33 boundaries are mostly fiat t i m e everything is flux

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

35 here time exists as part of the domain of the ontology

36 The SNAP Ontologies t1t1 t3t3 t2t2 here time exists outside the ontology, as an index or time-stamp

37 mereology works without restriction in every instantaneous 3-D section through reality

38 Three views/partitions of the same reality

39 all contain huge amounts of knowledge of this reality against Kant

40 The Time-Stamped (3-D) Ontology t1t1 t3t3 t2t2

41 each section through reality is to be conceived in presentist terms each section includes everything which exists at the corresponding now

42 Not in a Subject Substantial In a Subject Accidental Said of a Subject Universal, General, Type Second Substances man, horse, mammal Non-substantial Universals whiteness, knowledge Not said of a Subject Particular, Individual, Token First Substances this individual man, this horse this mind, this body Individual Accidents this individual whiteness, knowledge of grammar

43 Aristotle’s Ontological Square SubstantialAccidental Second substance man cat ox Second accident headache sun-tan dread First substance this man this cat this ox First accident this headache this sun-tan this dread Universal Particular

44 Aristotle’s Ontological Square SubstantialAccidental Second substance man cat ox Second accident headache sun-tan dread First substance this man this cat this ox First accident this headache this sun-tan this dread Universal Particular

45 Aristotle’s Ontological Square SubstantialAccidental Second substance man cat ox Second accident headache sun-tan dread First substance this man this cat this ox First accident this headache this sun-tan this dread Universal Particular

46 Aristotle’s Ontological Square SubstantialAccidental Second substance man cat ox Second accident headache sun-tan dread First substance this man this cat this ox First accident this headache this sun-tan this dread Universal Particular

47 Aristotle’s Ontological Square SubstantialAccidental Second substance man cat ox Second accident headache sun-tan dread First substance this man this cat this ox First accident this headache this sun-tan this dread Universal Particular

48 Refining the Ontological Square SubstantialAccidental Second substance man cat ox Second accident headache sun-tan dread First substance this man this cat this ox First accident this headache this sun-tan this dread Universal Particular

49 Refining the Ontological Square Substantial Dependent Entities Exercise of power Exercise of function Movement Action Substances Collectives Undetached parts Substantial boundaries Powers Functions Qualities Shapes Occurrents Continuants

50 Refining the Ontological Square Substantial Dependent Exercise of power Exercise of function Movement Action Substances Collectives Undetached parts Substantial boundaries Powers Functions Qualities Shapes Occurrents Continuants

51 Refining the Ontological Square Substantial Dependent Entities The big bang????Exercise of power Exercise of function Movement Action Processes Substances Collectives Undetached parts Substantial boundaries Powers Functions Qualities Shapes Occurrents Continuants

52 Refining the Ontological Square Substantial Dependent Entities John‘s reddening John‘s blushing John‘s bruising SPAN Substances Collectives Undetached parts Substantial boundaries John‘s redness John‘s blush John‘s bruise SNAP Occurrents Continuants

53 Refining the Ontological Square Substantial Dependent Entities John‘s reddening John‘s blushing John‘s bruising SPAN (perduring) Stuff (Blood, Snow, Tissue) Mixtures Holes John‘s redness John‘s blush John‘s bruise SNAP (enduring) Occurrents Continuants

54 A Refined Ontological Square Substantial Dependent Entities John‘s reddening John‘s professorship My knowledge of French SPAN (perduring) Stuff (Blood, Snow, Tissue) Mixtures Holes John‘s redness John‘s blush John‘s bruise SNAP (enduring) Occurrents Continuants

55 genus Species-genus trees can be represented also as map- like partitions

56 From Species to Genera canary animal bird

57 From Species to Genera animal bird canary

58 Species Genera as Tree canary animal bird fish ostrich

59 Species-Genera as Map/Partition animal bird canary ostrich fish canary

60 Tree and Map-Partitions Together

61 ‘Granularity’ in two senses: depth of a tree hierarchy resolution of a map-like partition

62 There are many different species-genus hierarchies  many different ways to cut through the complex thicket of invariant patterns in reality

63 Recall the distinct temporal partitions of reality as a whole

64 Coarse-grained Partition

65 Fine-Grained Partition

66 Basic Formal Ontology ? ? ?

67 Ontological Zooming

68 Universe/Periodic Table animal bird canary ostrich fish folk biology partition of DNA space

69 Universe/Periodic Table animal bird canary ostrich fish both are transparent partitions of one and the same reality

70 France Regions Departments

71 Perspectivalism Different partitions may represent cuts through the same reality which are skew to each other

72 An organism is a totality of molecules An organism is a totality of cells An organism is a single unitary substance... all of these express veridical partitions An organism is a totality of atoms

73 all express partitions which are transparent, at different levels of granularity, to the same reality beyond

74 Ontology like cartography must work with maps at different scales and with maps picking out different dimensions of invariants

75

76 If Aristotelian realism is right then there are very many map-like partitions, at different scales, which are all transparent to the reality beyond the mistake arises when one supposes that only one of these partitions is veridical

77 There are not only map-like partitions of reality into spatial chunks but also distinct partitions of reality into universals -- mutually compatible ways of providing inventories of universals (among proteins, among cells, among organisms …)

78 Varieties of granular partitions Partonomies: inventories of the parts of individual entities Maps: partonomies of space Taxonomies: inventories of the universals covering a given domain of reality

79 Periodic Table Periodic Table of Chemical Elements

80 Many partitions are transparent to reality TEE is a ragbag of skew partitions, some of them transparent One job of the ontological realist is to understand how different partitions of the same reality interrelate -- notion of projection

81 Contrast this with ‘knowledge representation’

82  problem of ‘knowledge representation’

83 problem of ‘knowledge representation’ solved by looking at the world

84 How solve the problem? Ontology as maximally opportunistic theory of reality (not of ‘knowledge’) -- address the same reality at different granularities

85 Maximally opportunistic means: don’t just look at beliefs look at the objects themselves from every possible direction, formal and informal, scientific and non- scientific …

86 BFO/MedO: Basic Formal Ontology and Medical Ontology Draft ( )

87 Basic Formal Ontology consists in a series of sub- ontologies (most properly conceived as a series of perspectives on reality), the most important of which are:

88 Basic Formal Ontology SnapBFO, a series of snapshot ontologies (O ti ), indexed by times SpanBFO a single videoscopic ontology (O v ).

89 SNAP and SPAN Each O ti is an inventory of all entities existing at a time. O v is an inventory (processory) of all processes unfolding through time. (Each O ti is thus analogous to anatomy; O v is analogous to physiology.)

90 SNAP and SPAN Each snapshot ontology represents a presentistic assay of the entities existing at some given present instant. O v is a (God’s eye) partition of the totality of processes.

91 Both SnapBFO and SpanBFO will serve as basis for a series of sub-ontologies at different levels of granularity. The same portion of reality may appear at a plurality of levels of granularity. Thus masses at one level may be aggregates at another level. What counts as a unitary process at one level may be part of a process- continuum at another level. Granularity

92 BFO applied to Medicine What follows is a preliminary taxonomic tree (inspired in part by LADSEB work) examples of medical entities are indicated in green as a first step towards expanding BFO to MedOMedO

93 SNAP: Entities existing in toto at a time

94

95

96 SNAP

97 SPAN: Entities extended in time

98 SPAN: Entities extended in time

99 SPAN: Entities extended in time

100 Each ontology above represents some partition of reality into categories or universals. Individual instances (tokens) are to be conceived as being located in cells of the diagrams.

101 The ontologies here indicated are partial only (they are windows on just that portion of reality which is visible through the given ontology).

102 Double-Counting A cell labeled * within a given ontology represents a category division which involves some double-counting in relation to the categories within the same ontology represented by cells not so labeled.

103 For example here

104 Spatial Regions The spatial regions acknowledged by SnapBFO are, on the mesoscopic level of granularity, the sorts of domesticated spatial regions referred to by expressions such as: ‘in the room’, ‘in the lung’, ‘on the table’, ‘in Poland’ etc. (Thus they are not the abstract spatial regions investigated by physics.)

105

106 Free and bound portions of space Free portions of space are spatial regions of the same (domesticated) kind but with no physical boundaries or retainers (such as walls, floor, ceiling). Bound portions of space can be bound either completely, as in the case of a closed room or an air- bubble inside your body, or partially, as in the case of a birdcage or nostril.

107 Free and bound portions of space Both free and bound portions of space retain their identity from one instant to the next even though they are projected in succession onto distinct abstract spatial regions in the physicist’s sense (just as substances retain their identity from one instant to the next even though they are projected in succession on distinct aggregates of molecules).

108 Behavior Settings The spatiotemporal regions acknowledged by SpanBFO are similarly regions determined by domesticated portions of space over (for example) clock or calendar time. They are the spatiotemporal regions occupied by behavior settings in Roger Barker’s sense (the 5pm train to Long Island, the early morning swim, your meeting with the Dean).

109 SPAN: Entities extended in time

110 Relational Dependent Entities Dependent entities, both within the SNAP and within the SPAN ontologies, are divided into: relational (for entities dependent on a plurality of entities) and non-relational (for entities dependent on a single entity).

111 Problems How are entities visible in the SPAN ontology related to entities visible in the SNAP ontologies (e.g. via dependence, participation, initiation, sustaining in being,etc.) How are entities visible in ontologies at different levels of granularity related to each other (most importantly: as part to whole)