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VT

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Ontology

Barry Smith

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Aristotle

author of The Categories

Aristotle

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From Species to Genera

canary

animal

bird

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Species Genera as Tree

canary

animal

bird fish

ostrich

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Species-genusgenus trees can be represented also as map-like partitions

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From Species to Genera

canary

animal

bird

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From Species to Genera

animal

bird

canarycanary

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Species Genera as Tree

canary

animal

bird fish

ostrich

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Species-Genera as Map/Partition

animal

bird

canary

ostrich

fish

canary

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If Aristotelian realism is right,

then such partitions are transparent to the reality beyond

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Tree and Map/Partition

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Alberti’s Grid

c.1450

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Coarse-grained Partition

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Fine-Grained Partition

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Scientific theories

comprehend in their underlying category systems veridical partitions of reality

often there are many veridical partitions of reality,

cross-cutting each other,

differing only in nuances)

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What is a gene?

GDB: a gene is a DNA fragment that can be transcribed and translated into a protein

Genbank: a gene is a DNA region of biological interest with a name and that carries a genetic trait or phenotype

(from Schulze-Kremer)

GO does not tell us which of these is correct, or indeed whether either is correct, and it does not tell us how to integrate data from the corresponding sources

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Question:

what other sorts of partitions have this feature of transparency?

the partitions of common sense (folk biology, folk physics, folk psychology ...)

Answer:

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Aristotle

the ontologist of common-sense reality

Aristotle

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The world we grasp in natural language

= the world as apprehended via that conceptualization we call common sense

= the normal environment (the niche) shared by children and adults in everyday perceiving and acting

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The world of mothers, milk, and mice ...

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The Empty Mask (Magritte)

mama

mouse

milk

Mount Washington

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our common-sense partition of the world of common sense is transparent

(common sense, like science, is [mostly*] true)

mothers exist ...

* “mostly” because of the problem of vagueness

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Problem of vagueness solved

by recognizing that our categories apply to reality in such a way as to respect an opposition

... between standard or focal or prototypical instances

... and non-standard or ‘fringe’ instances

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birds

ostrich

Natural categories have borderline cases

sparrow

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... they have a kernel/penumbra structure

kernel of focal

instances

penumbra of borderline cases

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animal

bird

canary

ostrich

fish

every cell in every common-sense partition is subject to this same kernel-penumbra structure:

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What is common-sense reality?

the mesoscopic space of everyday human action and perception

– a space centered on objects organized into hierarchies of species and genera

... and subject to prototypicality

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but more:

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in addition to objects (substances),

which pertain to what a thing is at all times at which it exists:

cow man rock planet

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the common-sense world contains also accidents

which pertain to how a thing is at some time at which it exists:

red hot suntanned spinning

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An accident

= what holds of a substance per accidens

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quid? substance quantum? quantity quale? qualityad quid? relationubi? placequando? timein quo situ? status/contextin quo habitu? habitusquid agit? actionquid patitur? passion

Nine Accidental Categories

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= relations of inherence(one-sided existential dependence)

John

hunger

Substances are the bearers of accidents

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Both substances and accidents

instantiate universals at higher and lower levels of generality

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siamese

mammal

cat

organism

substancespecies, genera

animal

instances

frog

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Common nouns

pekinese

mammal

cat

organism

substance

animal

common nouns

proper names

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siamese

mammal

cat

organism

substancetypes

animal

tokens

frog

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Our clarification

accidents to be divided into

two large and essential distinct families of

QUALITIES

and

PROCESSES

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There are universals

both among substances (man, mammal)

and among qualities (hot, red)

and among processes (run, movement)

There are universals also among spatial regions (triangle, room, cockpit)

and among spatio-temporal regions (orbit)

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Substance universals

pertain to what a thing is at all times at which it exists:

cow man rock planetVW Golf

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Quality universals

pertain to how a thing is at some time at which it exists:

red hot suntanned spinningClintophobic Eurosceptic

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Process universals

reflect invariants in the spatiotemporal world taken as an atemporal whole

football match

course of disease

exercise of function

(course of) therapy

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Processes and qualities, too, instantiate genera and species

Thus process and quality universals form trees

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Accidents: Species and instances

quality

color

red

scarlet

R232, G54, B24

this individual accident of redness (this token redness – here, now)

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substance

one substantial categoryJohn, man

nine accidental categorieshunger, your hunger, being hungryyour sun-tanyour being taller than Mary

accidents

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substance

place (in the Lyceum)

time (yesterday)

position (is sitting)

possession (has shoes on)

action (cuts)

passion (is cut)

quantity (two feet long)

quality (white)

relation (taller than)

John

accidents

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substance

Substances are the bearers of accidents

accidentsBearers

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substance

Substances are the bearers of accidents

accidents

John = relations of inherence(one-sided existential dependence)

Bearers

hunger

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s

substance

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Substance + Accident = State of Affairs

setting into relief

States of Affair

s

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instances

Prototypicality among instances too

albino frogalbino frog

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Aristotle 1.0

an ontology recognizing:substance tokensaccident tokenssubstance typesaccident types

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Is everything in common-sense reality either a substance or an accident?

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well, what about artefacts ?

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Standard Aristotelian theory of artefacts:

artefacts are mereological sums of substances

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Positive and negative parts

positivepart

negativepartor hole

(made of matter)

(not made of matter)

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quid? substance quantum? quantity quale? qualityad quid? relationubi? placequando? timein quo situ? status/contextin quo habitu? habitusquid agit? actionquid patitur? passion

Nine Accidental Categories

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Places

For Aristotle the place of a substance is the interior boundary of the surrounding body

(for example the interior boundary of the surrounding water where it meets a fish’s skin)

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What is missing from Aristotle?

Gibson: affordancesniches

Barker: behavior settings

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Places are holes

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niches, environments are holes

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The metaphysics of holes

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Aristotle 1.5

an ontology ofsubstances + accidents+ holes (and other entities not made of matter)+ fiat and bona fide boundaries+ artefacts and environments

is true

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folk biology

Aristotelian folk biology, folk physics, folk psychology, etc., are true of the common-sense world as it currently exists

(they have nothing to offer regarding its pre-history, its long term evolution, its position in the cosmos)

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reference vs. theory

They have not much to offer, either, by way of good explanatory theories of the entities in their respective domains,

but they are transparent to those domainsnonetheless

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reference realism vs. theory realism

this distinction applied not only to science (against T. S. Kuhn et al.) but also to common sense (against sceptics of various stripes)

the sun exists, and has existed for a long time – the very same object

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Both scientific partitions and common-sense partitions

are based on reference-systems which have survived rigorous empirical tests

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The $64000 Question

How do those parts and dimensions of reality which we call the common-sense world

... relate to those parts and dimensions of reality which are studied by science?

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Aristotle 2000

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Universe/Periodic Table

animal

bird

canary

ostrich

fishfolk biology

partition of DNA space

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Universe/Periodic Table

animal

bird

canary

ostrich

fish

both are transparent partitions of one and the same reality

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many transparent partitions

at different levels of granularity

will operate with species-genus hierarchies

and with an ontology of substances (objects) and accidents (attributes, processes)

along the lines described by Aristotle

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relative hylomorphism

substances and accidents reappear in the microscopic and macroscopic worlds of e.g. molecular biology and astronomy

(Aristotelian ontological zooming)

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we do not assert

that every level of granularity is structured in substance-accident form -- perhaps there are pure process levels, perhaps there are levels structured as fields

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Perspectivalism

PerspectivalismDifferent partitions may represent cuts through the same reality which are skew to each other

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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

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all express partitions which are transparent,

at different levels of granularity,

to the same reality beyond

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Coarse-grained Partition

what happens when a fringe instance arises ?

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Coarse-grained Partition

what happens when a fringe instance arises ?

Aristotle 1.0: you shrug your shoulders

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Aristotle 2000:you go out to find a finer grained partition which will recognize the phenomenon in question as prototypical

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The advance of science

is not an advance away from Aristotle towards something better.

Provided Aristotle is interpreted aright, it is a rigorous demonstration of the correctness of his ontological approach

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IFOMIS

Institute for Formal Ontology and Medical Information Science

Faculty of Medicine

University of Leipzig

http://ifomis.de

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The Idea

Computational medical research

will transform the discipline of medicine

… but only if communication problems can be solved

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Medicine

desperately needs to find a way

to enable the huge amounts of data

resulting from trials by different groups

to be (f)used together

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How resolve incompatibilities?

Ganze Industrie von ‘Ontologien’ in der heutigen Informationswissenschaft

“ONTOLOGY” = the solution of first resort (compare: kicking a television set)

But what does ‘ontology’ mean?Current most popular answer: a hierarchy of concepts (a thesaurus, a list of terms)

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First ontology

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

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Linnaean Ontology

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Medical Diagnostic Ontology

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Example: The Gene Ontology (GO)

hormone ; GO:0005179

%digestive hormone ; GO:0046659 %peptide hormone ; GO:0005180 %adrenocorticotropin ; GO:0017043 %glycopeptide hormone ; GO:0005181 %follicle-stimulating hormone ; GO:0016913

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as tree

hormone

digestive hormone peptide hormone

adrenocorticotropin glycopeptide hormone

follicle-stimulating hormone

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Gene Ontology

Cellular Component Ontology: subcellular structures, locations, and macromolecular complexes;examples: nucleus, telomere

Molecular Function Ontology: tasks performed by individual gene products; examples: transcription factor, DNA helicase

Biological Process Ontology: broad biological goals accomplished by ordered assemblies of molecular functions; examples: mitosis, purine metabolism

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Problem: There exist multiple databases

genomic cellular

structural phenotypic

… and even for each specific type of information, e.g. DNA sequence data, there exist several databases of different scope and organisation

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What is a gene?

GDB: a gene is a DNA fragment that can be transcribed and translated into a protein

Genbank: a gene is a DNA region of biological interest with a name and that carries a genetic trait or phenotype

GO does not tell us which of these is correct, or indeed whether either is correct, and it does not tell us how to integrate data from the corresponding sources

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Reference Ontology

An ontology is a theory of a domain of entities in the world

Ontology is outside the computer

seeks maximal expressiveness and adequacy to reality

and sacrifices computational tractability for the sake of representational adequacy

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Methodology

Get ontology right first

(realism; descriptive adequacy; rather powerful logic);

solve tractability problems later

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The Reference Ontology Community

IFOMIS (Leipzig) Laboratories for Applied Ontology (Trento/Rome,

Turin)Foundational Ontology Project (Leeds)Ontology Works (Baltimore)BORO Program (London)Ontek Corporation (Buffalo/Leeds)LandC (Belgium/Philadelphia)

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Recall:

GDB: a gene is a DNA fragment that can be transcribed and translated into a protein

Genbank: a gene is a DNA region of biological interest with a name and that carries a genetic trait or phenotype

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Ontology

Note that terms like ‘fragment’, ‘region’, ‘name’, ‘carry’, ‘trait’, ‘type’

… along with terms like ‘part’, ‘whole’, ‘function’, ‘substance’, ‘inhere’ …

are ontological terms in the sense of traditional (philosophical) ontology

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Three types of reference ontology

1. formal ontology = framework for definition of the highly general concepts – such as object, event, part – employed in every domain

2. domain ontology, a top-level theory with a few highly general concepts from a particular domain, such as genetics or medicine

3. terminology-based ontology, a very large theory embracing many concepts and inter-concept relations

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MedO

including sub-ontologies:

cell ontology

drug ontology

protein ontology

gene ontology

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and sub-ontologies:

anatomical ontology

epidemiological ontology

disease ontology

therapy ontology

pathology ontology

the whole designed to give structure to the medical domain

(currently medical education comparable to stamp-collecting)

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If sub-domains like these

cell ontology

drug ontology

protein ontology

gene ontology

are to be knitted together within a single theory,

then we need also a theory of granularity