1

Basic Formal Ontology

Barry Smithhttp://ontologist.com

March 2004

2

3

The problem

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

4

The solution

“ONTOLOGY”

Remove “Ontology Impedance”

But what does “ontology” mean?

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

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

Ontology a kind of generalized chemistry or zoology

(Aristotle’s ontology grew out of biological classification)

8

Aristotle

world’s first ontologist

9

World‘s first ontology

(from Porphyry’s Commentary on Aristotle’s Categories)

10

Linnaean Ontology

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

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

13

different concept/terminology systems

14

need not interconnect at all

for example they may relate to entities of different granularity

15

we cannot make incompatible terminology-systems interconnect

just by looking at concepts, or knowledge or language

16

we cannot make incompatible terminology-systems interconnect

by staring at the terminology systems themselves

17

to decide which of a plurality of competing definitions to accept

we need some tertium quid

18

we need, in other words,

to take the world itself into account

19

BFO

= basic formal ontology

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

The BFO framework

will solve the problem of ontological impedance and provide tools for quality-control on the output of computer applications

22

BFO not a computer application

but a Reference Ontology

(something like old-fashioned metaphysics)

23

Reference Ontology

a theory of a domain of entities in the world

24

BFOnot just a system of categoriesbut a formal theory with definitions, axioms, theoremsdesigned to provide the resources for

reference ontologies for specific domainsof sufficient richness that terminological incompatibilities can be resolved intelligently rather than by brute force

25

Proposed solutiondistinguish 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

Reference Ontology

a theory of the tertium quid

– called reality –

needed to hand-callibrate database/terminology systems

27

Methodology

Get ontology right first

(realism; descriptive adequacy; rather powerful logic);

solve tractability problems later

28

29

Realist Perspectivalism

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

30

Anatomy vs. Pathology

31

The Problem

The tumor developed in John’s lung over 25 years

32

The Problem

____ developed in _____ over 25 years

process

state

33

The Problem

The tumor developed in the lung over 25 years

substances

things

objects

continuants

34

The Problem

The tumor developed in John’s lung over 25 years

PARTHOOD NOT DETERMINATE

35

The Problem

The tumor developed in the lung over 25 years

substances

GLUING THESE TOGETHER YIELDS ONTOLOGICAL MONSTERS

processes

36

Substances and processes exist in time in different ways

substance

t i m

e

process

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

No way in which sums of substances and processes can exist in time

… hence

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

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

Fourdimensionalism (the SPAN perspective) is right in

everything it says

But incomplete

42

Realist Perspectivalism

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

43

Need for different perspectives

Not one ontology, but a multiplicity of complementary ontologies

Cf. particle vs. wave ontologies in quantum mechanics

44

Two Orthogonal, Complementary Perspectives

SNAP and SPAN

45

Snapshot Video ontology ontology

substance

t i m

e

process

46

SNAP and SPANstocks and flows

commodities and services

product and process

anatomy and physiology

47

SNAP and SPANSNAP 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

You are a substance

Your life is a process

You are 3-dimensional

Your life is 4-dimensional

49

Many SNAP Ontologies

t1

t3t2

here time exists outside the ontology, as an index or time-stamp

50

each SNAPi section through reality

includes everything which exists (present tense)

51

mereology works without restriction (parthood is everywhere determinate) in

every SNAPi ontology

52

Three kinds of SNAP entities

1. Substances (Independent)

2. SNAP Dependent Entities

3. Spatial regions, contexts, niches, environments

53

SNAP dependent entities

States, powers, qualities, roles …

functions, dispositions, plans, shapes, status, habitus, liabilities …

= dependent SNAP entities

54

SNAP dependent entities:

one-place:

your temperature, color, heightmy knowledge of French

the whiteness of this cheese the warmth of this stone

the fragility of this glass

55

relational SNAP dependent entities

John Mary

love

stand in relations of one-sided dependence to a plurality of substances simultaneously

specific dependence

56

Three kinds of SNAP entities

1. Substances

2. Dependents

3. Spatial regions, contexts, niches, environments

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

59

SNAP: Entities existing in toto at a time

60

The SPAN Ontology

t i m e

61

here time exists as part of the domain of the ontology

The SPAN ontology

62

mereology works without restriction everywhere here

t i m e

clinical trial

63

Processes, too, are dependent on substances

One-place vs. relational processes

One-place processes:

your getting warmer

your getting hungrier

64

Examples of relational processes

kissings, thumpings, conversations,

dancings,

join their carriers together into collectives of greater or lesser duration

65

SPAN: Entities extended in time

SPANEntity extended in time

Portion of Spacetime

Fiat part of process *First phase of a clinical trial

Spacetime worm of 3 + Tdimensions

occupied by life of organism

Temporal interval *projection of organism’s life

onto temporal dimension

Aggregate of processes *Clinical trial

Process[±Relational]

Circulation of blood,secretion of hormones,course of disease, life

Processual Entity[Exists in space and time, unfolds

in time phase by phase]

Temporal boundary ofprocess *

onset of disease, death

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

Two kinds of SPAN entities

1. Processes (including events: process-boundaries, settings)

2. Spatio-temporal regions

68

Settings = 4-dimensional environments

Lobsters have evolved into environments marked by cyclical patterns of temperature change

Tudor EnglandThe Afghan winterThe window of opportunity for an invasion of Iraq

69

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

70

problem cases

forest fire

anthrax epidemic

hurricane Maria

traffic jam

ocean wave

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

The Epidemic (SNAP)

The Spread of an Epidemic (SPAN)

73

Material examples:

performance of a symphonyprojection of a filmexpression of an emotionutterance of a sentenceapplication of a therapycourse of a diseaseincrease of temperature

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

How link SNAP and SPAN together?

via formal relations

= entities which do not add anything to being

76

Successive Causality

SNAP-SPAN: Agent causationA substance produces causally a process

SPAN-SPAN: Process causationOne process causes another process

SPAN-SNAP: Causal repercussionA process results in the modification of a substance (always mediated by process causation)

SNAP-SNAP: Causal originOne substance is the causal origin of another (mediated by other types of causal relations)

77

Successive Causality

SNAP-SPAN: Agent causation

SPAN-SPAN: Process causation

SPAN-SNAP: Causal repercussion

SNAP-SNAP: Causal origin

78

Simultaneous causality

SPAN-SPAN

The rise in temperature causes the (simultaneous) increase in pressure

(Boyle’s law)

79

Substance Process

PARTICIPATION(a species of dependence)

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

Axes of variation

activity/passivity (agentive)

direct/mediated

benefactor/malefactor (conducive to existence) [MEDICINE]

82

SNAP-SPAN

Participation

Perpetration (+agentive)

Initiation

Perpetuation

Termination

Influence

Facilitation

Hindrance

Mediation

Patiency(-agentive)

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

Initiation

A substance initiates a process:

The referee starts the race

The attorney initiates the process of appeal

85

Perpetuation

A substance sustains a process:

The singer sings the song

The charged filament perpetuates the emission of light

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

Influence

A substance (or its quality) has an effect on a process

The steepness of the slope affects the movement of the troopsThe politicians influence the course of the war

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

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

Patiency

Dual of agentive participation

John kisses [Mary] (John agent)

Mary is kissed [by John] (Mary patient)

91

Signatures of meta-relations

SNAP Component SPAN Component

Substances

SPQR…

Space Regions

Processuals

Processes

Events

Space-Time Regions

92

Signatures of meta-relations

SNAP Component SPAN Component

Substances

SPQR…

Space Regions

Processuals

Processes

Events

Space-Time Regions

93

Signatures of meta-relations

SNAP Component SPAN Component

Substances

SPQR…

Space Regions

Processuals

Processes

Events

Space-Time Regions

94

Signatures of meta-relations

SNAP Component SPAN Component

Substances

SPQR…

Space Regions

Processuals

Processes

Events

Space-Time Regions

95

REALIZATION

96

Signatures of meta-relations

SNAP Component SPAN Component

Substances

SPQR…

Spatial Regions

Processuals

Processes

Events

Space-Time Regions

participation

realization

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

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

SPQR… entities and their SPAN realizations

plan

function

role

disposition

algorithm

SNAP

100

SPQR… entities and their SPAN realizations

execution

expression

exercise

realization

application

course

SPAN

101

SNAP SPAN

Participation

Substance Process

Realization

SPQR Process

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

Sustaining in being

A process sustains in being a substance:

The circulation of the blood sustains the body

Levying taxes sustains the army

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

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

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

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

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

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

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

SNAP-SPAN

Participation

Perpetration (+agentive)

Initiation

Perpetuation

Termination

Influence

Facilitation

Hindrance

Mediation

Patiency(-agentive)

112

SPAN-SNAP

Involvement

Creation

Sustenance

Destruction

Continuation

DegradationDestruction

Creation

DemarcationBlurring

Qualitative projection

Degradation

113

Realist Perspectivalism

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

114

Cardinal Perspectives

SNAP vs. SPAN

Granularity (Micro vs. Meso vs. Macro)

115

Cardinal Perspectives

SNAP vs. SPAN

Granularity (Micro vs. Meso vs. Macro)

116

 

Ontological Zooming

117

Ontological Zooming

human anatomy

cellular anatomy

118

Part-Whole

Basic relation exclusively intra-ontological: either SNAP-SNAP or SPAN-SPAN.

SNAP-SNAP: only if SNAPis have the same temporal index

119

Relations crossing the SNAP/SPAN border are never part-relations

John’s lifesubstance John

physiological processes

sustaining in existence

120

Granularity

spatial region substance

parts of substances are always substances

121

Granularity

spatial region substance

parts of spatial regions are always spatial regions

122

Granularity

process

parts of processes are always processes

123

Intra-granular and cross-granular parthood

across SNAPs:Kevin’s arm is part of KevinKevin’s molecule is part of Kevin

across SPANs:Kevin’s leg-movement is part of Kevin’s runningKevin’s cytometabolism is part of Kevin’s running

124

THE END