IFOMIS Projects
1. Basic Formal Ontology
2. Ceusters
3. Medical Being
1
1. Basic Formal Ontology
mereotopology
dependence
granularity/partition theory
SNAP/SPAN
action/participation
plans/functions/executions
causality/powers/dispositions
environment
normativity
2
2. Ceusters
unstructured patient records as basis for a
cosmic medical experiment
We provide formal-ontological services for
Ceusters
He provides powerful software tools and
influential support in our fight for good
ontology in the medical informatics domain
3
Rules for Good Ontology
These are rules of thumb:
They represent ideals to be
approximated to in practice
(and often come with trade-offs)
4
3. Medical Being
MedO
many MedOs
BFO: SNAPs, SPAN(s), granularity
MedO: SNAPs, SPAN(s), granularity
different bodily systems
total bodily system
5
OUTPUT
1. Basic Formal Ontology
collaboration with B. Bennett re axiom
systems
conference presentations
many publications in good journals
2. Ceusters
ontology software tools for medical NLP
3. Medical Being
a big book
6
Medical Being
mereotopology: Schubert (anatomy with holes)
dependence
granularity/partition theory: molecules, cells …
SNAP/SPAN: anatomy, physiology …
action/participation: doctor, patient …
plans/functions/executions: therapy, application of
therapy …
causality/powers/dispositions: placebo effect …
normativity: health, disease, ‘normal’ liver
environment: environmental influences on disease
7
Medical Being
a book,
a textbook of medical ontology
for pedagogical purposes
for testing purposes (applied formal ontology)
as a showcase of good ontological methods
8
Chapters
Main Body Systems
structural system:
bones, muscles, connective tissue
skin and hair
circulatory system:
heart, veins, arteries, blood
digestive system
intestinal system
urinary system
9
Chapters
Main Body Systems (contd.)
nervous system
respiratory system
immune system
How do these systems relate together?
(a medico-ontological analogue of the mindbody problem)
10
Chapters
Embryonic Development
Sexual Reproduction
Birth
Childhood
Adolescence
Aging
Coma
Death
11
Chapters
Health
Disease
Infection
Accident, Injury, Wound
Epidemiology
12
Chapters
Sleep, anaesthesia, coma
Pain, Consciousness, Empathy, Sympathy
Mental illness
Therapy (null therapy)
Cure
Drug
Recuperation
13
Chapters
Antigens
viruses
bacteria
Parasites
Food
Alcohol
14
The ontologist’s job
is not to mimic or replace or usurp science
not to discover statistical or functional laws
it is to establish the categories involved in given
domains of reality and the relations between
them
via:
taxonomies
and:
partonomies
and by addressing NORMATIVE ISSUES such
as: what holds in the standard case
15
Naturalness
A good ontology should include in its basic
category scheme only those categories
which are instantiated by entities in reality
(it should reflect nature at its joints)
16
A good first test:
the categories in question should be
reflected in TEE
(for: Technically Extended English
= English as extended by the various
technical vocabularies of medical and
scientific disciplines)
17
Basic categories
are reflected by morphologically simple terms:
dog
pain
foot
blood
hunger
hot
red
diabetes
18
No theoretical artifacts
A good ontology should not include in its
basic category scheme
artifacts of logical, mathematical or
philosophical theories (such as: transfinite
cardinals, instantaneous rabbit-slices, nonexistent golden mountains, functions
across possible worlds, and the like).
19
Problem cases:
Fictional entities?
Absences?
Holes?
20
A good category scheme
a
should not be a mish-m sh of natural and
philosophical taxa
(keep views separate:
basic views, domain-specific views,
theoretical-artefactual views)
21
Perspectivalism
Perspectivalism
Different partitions may represent
cuts through the same reality which
are skew to each other
22
Ontology
like cartography
must work with maps at different scales and
with maps picking out different dimensions
of invariants
23
24
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
25
Cheese-paring principle
While a good ontology should use
categories which reflect only TEE, it
should also have the resources to do
justice to the fact that the world can be
sliced in many ways, including ways not
reflected by TEE
26
Example of cheese-paring
substance
action
(relational
process)
agent
(substance
plus role)
substance
patient
(substance
plus role)
linked by mutual dependence
27
Always ask the question
when is this proposition true?
when does this entity exist?
Different sorts of answers:
at ti (for SNAP entities)
------------------------------------------timelessly = looking down on the order of
time from the outside (for SPAN entities)
------------------------------------------through the time interval [ti,tj] ?
28
John lived in Kansas for 25 years
when is this proposition true?
when does the entity which makes it true
exist?
The problem with states of affairs is that they
are not mereologically determinate:
What are the parts of the state of affairs that
John lived in Kansas for 25 years
29
Against Sentences
Nouns and verbs are in order as they stand
The mereological indeterminacy of states of
affairs goes hand in hand with the
ontological perversity of the sentence
30
Everything
within SNAP is mereologically determinate
Everything
within SPAN is mereologically determinate
31
Sums within SNAP are always
mereologically determinate
John plus his role: Major John
John plus his quality: hungry John
John plus his disease: diabetic John, John
the case of diabetes
32
Sums within SPAN are always
mereologically determinate
The course of John’s disease plus the
course of John’s treatment plus the course
of John’s recuperation
The first half of the match
33
Double-Counting
in realm of substances
person
*ear, nose, throat, arm
*family, clinical trial population
fiat parts and aggregates should be
explicitly marked as involving doublecounting
34
Double-Counting
in realm of processes
process
*beginning, end, first phase
*series of clinical trials, World Cup
fiat parts and aggregates on the same
level of granularity should be explicitly
marked as involving double-counting
35
Rule:
Always mark cases of double-counting
wherever this occurs within a single ontology.
Double-counting is perfectly acceptable when
we are using more than one ontologies
simultaneously (yielding separate views of one
and the same reality)
Varzi: An inventory of reality should involve no
double-counting
(this principle is unsustainable)
36
SNAPshot ONTOLOGY
Enduring Entity
[Exists in space and time,
has no temporal parts]
Spatial Region
of Dimension 0,1,2,3
Dependent Entity
Independent Entity
Quality, State
Free Portion of Space
Your redness, my tallness, the cat’s being on the mat
[Sometimes form Quality Regions or Scales]
Physically Bound Portion of Space
Hole, niche, place
Quasi-Quality, Quasi-State
Price, debt, contract, a state of being married,
Role, Function, Power, Disposition
Stationary
Room, porch
Mobile
Cockpit, lung
[Have realizations (called: Processes)]
Quasi-Role/Function/Power
Plans, the functions of the President
Substance
[maximally connected causal unity]
Aggregate of Substances
(includes masses of stuff? liquids?)
*
Fiat Part of Substance
Nose, ear, mountain
*
*
Boundary of Substance
Fiat or Bona Fide or Mixed
Quasi-Substance
Church, college, clinic
37
SPAN ONTOLOGY
Concrete Entity
[Exists in space and time,
unfolds in time phase by phase]
Processual Entity
Process
Exercise of role, function, power
Aggregate of Processes
Fiat Part of Process
Spatio-Temporal Region
of Dimension T, T+0, T+1, T+2, T+3
Behavior settings
*
*
Instantaneous Temporal Boundary of Process
(= Ingarden’s 'Event’)
*
Quasi-Process
Course of treatment, clinical trial, tennis match
38
SPAM ONTOLOGY
Enduring Entity
[Exists in space
and time,
Spatial
has no temporal
Region
Quality, State Independe
Depende parts]
Substance
of
nt Entity Your redness, my nt Entity
[maximally
DimensionFree Portion of
tallness, the cat’s being
Aggregate of
on the mat
SpaceBound
connected causal
0,1,2,3Physically
[Sometimes form Quality
Substances
unity]
Role, Function,
Portion of Space
Regions or Scales]
Station
Fiat Part of Substance
(includes masses of
Power,QuasiDisposition
Mobile
Hole,
niche,
place
ary
Boundary
of
[Have realizations
stuff?
liquids?)
Cockpi
Role/Function/Pow
Spatio-Temporal
Room,
Processual
(called:
Processes)]
t, lung
er
Nose,
ear, mountain
Region Concrete Entity porch
Substance
Entity
Plans,
the
of Dimension T,[Exists
T+0, in space and
Quasi-Substance
Fiat
or Bona Fide or
Process
Processua
functions of the
Concrete Entity
T+1,
T+2, T+3
Church,
college,
Mixed
Exercise of role, function,
time,
Quasi-Quality, Quasi-State
l Entity
President
Process
clinic
time,
Behavior
settings
power [Exists in space and
Price, debt, contract, a state of
unfolds in time phase
Exercise of role,
unfolds in time phase by phase]
being married,
by phase]
function,
power
Aggregate
of
Aggregate of Processes
Spatio-Temporal
*
*
*
*
Processes
Fiat Part of Process
Instantaneous Temporal
Quasi-Process
Boundary
of Process
Course of treatment, clinical trial, tennis
(= Ingarden’s 'Event’)
match
*
*
Region
*Fiat Partof Dimension
T, T+0,
of
T+1, T+2, T+3
Instantaneous Temporal
ProcessBehavior settings
Boundary of Process
Quasi-Process
(=Course
Ingarden’s
'Event’)
of treatment,
clinical trial, tennis
match
*
*
39
Core Categories
are those categories of an ontology which
survive when all cases of double counting
have been eliminated
40
Rule: No Crossing Categories
If C is a core category then an instance of C
is always an instance of C whichever view
of C we take
If C is a core category then an instance of C
is always an instance of C whichever
granularity we take
If C is a core category then all parts and
aggregates of instances of C are also
instances of C
41
Determinables and Determinates
Determinable: color
Determinate: this particular shade of redness
(holds for tokens and for types)
Determinable: John’s temperature
Determinate: John’s temperature of 62 degrees
(The value is changing all the time)
42
Rule:
If x instances a category under any
determinable, then it instances this
category under all determinables
John’s temperature is a quality (a SNAP
entity)
The value of John’s temperature at a time is
a quality (a SNAP entity)
(This is so even if this value is changing
43
continuously)
Rule: Respect Granularity
spatial region
substance
quality
parts of spatial regions are always spatial regions44
Respect Granularity
spatial region
substance
quality
parts of substances are always substances
45
Respect Granularity
spatial region
substance
quality
parts of qualities are always qualities
46
Relations crossing the SNAP/SPAN
border are not part-relations
substance John
John’s life
physiological
processes
47
Relations between entities at
different granularities
are part relations
Hence we have two sorts of part-relations:
1. within a granularity
2. between granularities
Where granularities start and stop is
determined:
by the formation of scientific disciplines
by fiat?
48
Rule for Crossing Granularities
For x and y instances of core categories
If x is part of y, then x is of the same core category
as y
(if x is substantial, then y is substantial)
(if x is a quality, then y is a quality)
(if x is a process, then y is process)
(if x is a spatial region, then y is a spatial region)
(if x is a spatial boundary, then y is a spatial
boundary)
49
Rule for Crossing Granularities
For x an instances of a basic category, x is always
an instance of that category in every view or
from every perspective
(if x is substantial, then y is substantial)
(if x is a quality, then y is a quality)
(if x is a process, then y is process)
(if x is a spatial region, then y is a spatial region)
(if x is a spatial boundary, then y is a spatial
boundary)
50
How to treat cross-categorial
structures?
which ontology do they belong to?
How to treat higher-order attributions
Universals have instances
Universal A depends for its instantiation on
the instantiation of universal B
Roughly: these are meta-assertions
(that they have special truthmakers of their
own is an illusion of language)
51
Universals have instances
is not an extra assertion
rather it is something which shows itself via
the syntax of a good ontological language
(cf. Wittgenstein’s Tractatus)
52
Rules for good syntax in
formalizing ontology
entities of the same category should be
represented by means of symbols of the
same type
some symbols will not represent entities at
all (V, , =, , etc.)
53
Tools are just tools
If specific logical or mathematical or
conceptual tools are needed, for example
for semantic purposes,
then these should be clearly recognized as
tools and thus not be seen as having
consequences for basic ontology.
(Possible worlds …)
54
Trade off between cheese-paring
and sake-mongering
We can cut the cheese in many ways
But when we say
“For Pierre’s sake …, for Ingvar’s sake …”
then
There are no sakes in this room
And this is so however we cut the cheese
55
Problems arise for partial ontologies
only if they come along with the claim to
be complete
(reductionists are nearly always correct in
what they hold to exist -but incorrect when they hold that nothing
else exists)
56
Even reductionists
are right as far as they go
(even their peculiar maps of reality,
as consisting of processes,
or of spacetime worms,
are transparent to reality)
The only problem with such maps is that
they are not complete
57
Rules Governing Taxonomies
Every (coherent, tested) ontology for
a given domain at a given level of
granularity
should be representable as a tree in
the mathematical sense
Problem cases: shapes, colors ?
58
Natural scientific classifications are
principled
59
Principled classifications satisfy the
no-diamonds rule:
A
E
F
B
C
G
D
H
Good
Bad
60
Counterexample in the realm of
artifacts ?
urban structures
buildings
car parks
multi-story car-parks
61
Eliminating counter-examples
urban structures
buildings
parking areas
multi-story car-parks
“Ontoclean”
62
Rule: No ‘others’
All category labels should be positive
No category labels like:
entities which do not fall under the other
categories
63
Rule: Representations
A representation is never identical with the
object which it is a representation of
64
Rule: Fallibilism
Ontologists are seeking principles that are
true of reality,
but this does not mean that they have
special powers for discovering the truth.
Ontology is, like physics or chemistry, part
of a piecemeal, on-going process of
exploration, hypothesis-formation, testing
and revision.
65
Fallibilism
Ontological claims advanced as true today
may well be rejected tomorrow in light of
further discoveries or of new and better
arguments
Ontology is like a small window on reality
which, in fits and starts, gets bigger and
more refined as we proceed
66
Rule: Adequatism
A good ontology should be adequatist:
its taxonomies and partonomies should
comprehend the entities in reality at all levels
of aggregation,
from the microphysical to the cosmological,
and including also the middle world (the
mesocosmos) of human-scale entities in
between.
Adequatists: Aristotle, Ingarden, Chisholm; Johansson,
Smith
67
Nothing in life is certain
except
death
and taxes
Fictionalism is always wrong
Either an entity exists, or it does not exist
Either an entity type exists, or it does not exist
68
Quine is wrong
There is no entity without identity
We have no identity criteria for
people
taxes
plans
diseases
69
Quine is wrong
Quine’s slogan
-- “no entity without an identity criterion” -represents a confusion of ontology and
epistemology
Compare: “no truth without a truth criterion”
70
A good category scheme
a
should not be a mish-m sh of individuals
and universals
Universals are not extra types of entities
Types of entities ARE universals
Boxes in category diagrams represent
universals
The instances are what the boxes contain
71
SNAPshot ONTOLOGY
Enduring Entity
[Exists in space and
time,
has no temporal parts]
Dependent Entity
Independent Entity
Quality, State
Your redness, my tallness, the cat’s being on
the mat
[Sometimes form Quality Regions or Scales]
Substance
Dog
Cat
Quasi-Quality, Quasi-State
Price, debt, contract, a state of being
married,
Role, Function, Power, Disposition
[Have realizations (called: Processes)
Quasi-Role/Function/Power
Plans, the functions of the President
72
SNAPshot ONTOLOGY
Enduring Entity
[Exists in space and time,
has no temporal parts]
Dependent Entity
Independent Entity
Quality, State
Substance
Your redness, my tallness, the cat’s being on the mat
[Sometimes form Quality Regions or Scales]
Quasi-Quality, Quasi-State
Price, debt, contract, a state of being married,
Dog
Cat
Universal
Role, Function, Power, Disposition
[Have realizations (called: Processes)]
Quasi-Role/Function/Power
Plans, the functions of the President
73
Tree structure
Higher nodes within the tree represent
more general universals, lower nodes
represent less general universals.
74
Branches connecting nodes represent the
relations of inclusion of a lower category in
a higher:
man is included in mammal
mammal is included in animal
and so on.
75
An Ontology (Taxonomy) should be
Principled
Suppose that in counting off the cars passing
beneath you on the highway, your checklist
includes one box labeled red cars and another
box labeled Chevrolets.
The resultant inventory will be unprincipled;
you will almost certainly be guilty of counting
some cars twice.
Unprincipled = the two modes of classification
belong to two distinct classifications made for
two distinct purposes
76
An Ontology (Taxonomy) should be
Principled
Principled = Constructed for a single purpose
Principled = Generative (recursive?)
Principled = Double-counting clearly marked
Principled = SNAP-SPAN opposition reflected (so
mereological determinateness is guaranteed)
Principled = Clear rules when a new category must be
admitted
What else?
CYC is not principled
77
Tree structure implies:
A good ontology should satisfy certain
well-formedness rules
78
Well-formedness rule
Each tree is unified
in the sense that it has a single top-most
or maximal node, representing the
maximum category
comprehending all the categories
represented by the nodes lower down the
tree
79
Why trees?
A taxonomy (ontology) with two maximal
nodes would be in need of completion by
some extra, higher-level node
representing the union of these two
maxima.
Otherwise it would not be one taxonomy at
all, but rather two separate taxonomies
(e.g. SNAP and SPAN)
80
‘Entity’
= label for the highest-level category of
ontology.
Everything which exists is an entity
Alternative top-level terms favored by
different ontologists: ‘thing,’ ‘object,’ ‘item,’
‘element,’ ‘existent.’
Use of ‘entity’ is dangerous (see Frege)
81
Rule: Seek to establish a basis in
minimal nodes (leaves)
Leaves of the tree represent the lowest
categories (infima species)
= categories in which no sub-categories are
included.
‘Has a basis in minimal nodes’ = the
categories at the lowest level of the tree
exhaust the maximum category
82
Rule: Aim for Exhaustiveness
The chemical classification of the noble
gases is exhausted by:
Helium, Neon, Argon, Krypton, Xenon and
Radon.
…normally very hard to achieve
83
For a taxonomy with a basis in
minimal nodes
every intermediate node in the tree is
identifiable as a combination of minimal
nodes.
84
More well-formedness principles
There should be a finite number of steps
between the maximal category and each
minimal category.
There should be the same number of steps
between the topmost node of the tree and
all its lowest-level nodes.
85
Well-Formedness
The taxonomy as a whole is thereby divided
into homogeneous levels,
each level represents a jointly exhaustive
and pairwise disjoint partition of the
corresponding domain of categories on the
side of objects in the world.
86
Which rules satisfied by BFO?
Entity in 4-D Ontology
[Perdure. Unfold in Time]
Entity in 3-D Ontology
[Endure. No Temporal Parts]
Spatial Region
of Dimension 0,1,2,3
Independent Entity
Dependent Entity
Quality (Your Redness, My Tallness)
[Form Quality Regions/Scales]
Processual Entity
Spatio-Temporal Region
Dim = T, T+0, T+1, T+2, T+3
Substance
[maximally connected causal unity]
Process [Has Unity]
Clinical trial; exercise of role
Aggregate of Substances *
(includes masses of stuff? liquids?)
Aggregate of Processes*
Role, Function, Power
Have realizations (called: Processes)
Fiat Part of Substance *
Nose, Ear, Mountain
Fiat Part of Process*
Quasi-Role/Function/Power
The Functions of the President
Boundary of Substance *
Fiat or Bona Fide or Mixed
Instantaneous Temporal Boundary of
Process (= Ingarden’s 'Event’)*
Quasi-Substance
Church, College, Corporation
Quasi-Process
John’s Youth. John’s Life
Quasi-Quality
Prices, Values, Obligations
87
Types of Formal Relation
Intracategorial
– Mereological (part)
– Topological (connected, temporally precedes)
– Dependency (e.g. functional ?)
Intercategorial
– Inherence (quality of)
– Location
– Participation (agent)
– Dependency (of process on substance)
88
Relations can also hold across
granularities
Microbial processes in the human body
sustain the human body in existence
Neurophysiological processes in the brain
cause and provide the substratum for
cognitive processes
89
Trees of universals
(species-genus hierarchies)
capture the way the world is (realism)
– they depict the invariant
structures/patterns/regularities in reality
90
BUT: species-genus hierarchies
may capture the way the world should
be
– by depicting the
structures/patterns/regularities in the
realm of standards, ideal cases,
recipes
(a hierarchy of medical therapies)
91
TEEcentric (Aristotelian)
Realism
The general terms of TEE (or many of
them),
including terms like ‘Coca Cola’,
correspond to universals (species and
genera, invariant patterns) in reality
92
Two distinct realms of being
universals
particulars
general
individual
types
tokens
species
instances
essence
fact
93
species,
genera
substance
organism
animal
mammal
cat
siamese
frog
instances
94
common
nouns
Common nouns
substance
organism
animal
mammal
cat
pekinese
proper names
95
types
substance
organism
animal
mammal
cat
siamese
frog
tokens
96
Accidents: Species and instances
animal
substance
types
mammal
human
Irishman
this individual token man
tokens
97
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)
98
Substance universals
pertain to what a thing is at all times
at which it exists:
cow man rock planet
VW Golf
99
Quality universals
pertain to how a thing is at some time
at which it exists:
red hot suntanned spinning
Clintophobic Eurosceptic
100
Process universals
reflect invariants in the spatiotemporal
world taken as an atemporal whole
football match
course of disease
exercise of function
(course of) therapy
101
Processes and qualities, too,
instantiate genera and species
Thus process and quality universals
form trees
102
Accidents: Species and instances
quality
color
red
scarlet
R232, G54, B24
this individual accident of redness
(this token redness – here, now)
103