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Ontology
Barry Smith
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Aristotle
Aristotle
author of The Categories
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From Species to Genera
animal
bird
canary
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Species Genera as Tree
animal
bird
canary
fish
ostrich
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Species-genus trees can be
represented also as map-like
partitions
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From Species to Genera
animal
bird
canary
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From Species to Genera
animal
bird
canary
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Species Genera as Tree
animal
bird
canary
fish
ostrich
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Species-Genera as Map/Partition
animal
bird
fish
canary
ostrich
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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?
Answer:
the partitions of common sense (folk
biology, folk physics, folk psychology ...)
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Aristotle
Aristotle
the ontologist of common-sense reality
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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)
milk
mama
mouse
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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Natural categories have borderline
cases
sparrow
ostrich
birds
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... they have a kernel/penumbra
structure
penumbra of borderline cases
kernel of
focal
instances
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every cell in every common-sense partition is
subject to this same kernel-penumbra structure:
animal
bird
fish
canary
ostrich
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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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Nine Accidental Categories
quid?
quantum?
quale?
ad quid?
ubi?
quando?
in quo situ?
in quo habitu?
quid agit?
quid patitur?
substance
quantity
quality
relation
place
time
status/context
habitus
action
passion
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Substances are the bearers of accidents
hunger
John
= relations of inherence
(one-sided existential dependence)
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Both substances and accidents
instantiate universals at higher and lower
levels of generality
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species,
genera
substance
organism
animal
mammal
cat
siamese
frog
instances
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common
nouns
Common nouns
substance
organism
animal
mammal
cat
pekinese
proper names
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types
substance
organism
animal
mammal
cat
siamese
frog
tokens
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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 planet
VW Golf
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Quality universals
pertain to how a thing is at some
time at which it exists:
red hot suntanned spinning
Clintophobic 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
accidents
one substantial category
John, man
nine accidental categories
hunger, your hunger, being hungry
your sun-tan
your being taller than Mary
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substance
John
accidents
quantity (two feet long)
quality (white)
time (yesterday)
position (is sitting)
relation (taller than)
place (in the Lyceum)
possession (has shoes on)
action (cuts)
passion (is cut)
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substance
Bearers
accidents
Substances are the bearers of accidents
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substance
Bearers
accidents
Substances are the bearers of accidents
hunger
John
= relations of inherence
(one-sided existential dependence)
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substance
s
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Substance + Accident
= State of Affairs
States of Affair
setting into relief
s
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Prototypicality among
instances too
albino frog
instances
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Aristotle 1.0
an ontology recognizing:
substance tokens
accident tokens
substance types
accident types
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Is everything in commonsense 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
positive
part
(made of matter)
negative
part
or hole
(not made
of matter)
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Nine Accidental Categories
quid?
quantum?
quale?
ad quid?
ubi?
quando?
in quo situ?
in quo habitu?
quid agit?
quid patitur?
substance
quantity
quality
relation
place
time
status/context
habitus
action
passion
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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: affordances
niches
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 of
substances + 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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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 domains
nonetheless
reference vs. theory
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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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animal
Universe/Periodic Table
bird
fish
folk biology
canary
ostrich
partition of DNA space
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animal
Universe/Periodic Table
bird
fish
canary
ostrich
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
Perspectivalism
Different partitions may represent
cuts through the same reality which
are skew to each other
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An organism is a totality of atoms
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
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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
adrenocorticotropin
peptide hormone
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 stampcollecting)
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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
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