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ECO
R
European Centre for
Ontological Research
Realist Ontology for the
Semantic Web:
Applications in
Biomedical Informatics
Werner Ceusters
European Centre for Ontological Research
Universität des Saarlandes
Saarbrücken, Germany
ECO
R
European Centre for
Ontological Research
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Lecture overview
Credentials
The many faces of “ontology”
Realist ontology
Why is the concept-based approach so widespread ?
The price you pay if you go for concepts ...
Can Description Logics save the world ?
And then there was OWL
Take home messages
ECO
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European Centre for
Ontological Research
European Centre for
Ontological Research
External
members
Local members
Partners
Status Dec 2, 2004
ECO
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European Centre for
Ontological Research
European Centre for
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Directors
Management Board
Member representatives
Advisory
Board
Status Dec 2, 2004
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Institute for Formal Ontology
European Centre for
Ontological Research
and Medical Information Science
• an interdisciplinary research group
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Philosophy,
Computer and Information Science,
Logic,
Medicine,
Medical Informatics.
• a center of theoretically grounded research in
both formal and applied ontology.
• Main goal: to develop a formal ontology that will
be applied and tested in the domain of medical
and biomedical information science.
ECO
R
European Centre for
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IFOMIS competences
•Logics
•Logics
•Informatics
•Spatio-temporal reasoning
•Medicine
•Knowledge engineering
•Formal
•Formal Ontology
Ontology//metaphysics
metaphysics
•Mathematics
•Qualitative spatial reasoning
•Ontological engineering
•History
•Historyofofphilosophy
philosophy
•Philosophy
•Philosophy of
of science
science
•Linguistics
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Status Dec 2, 2004
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Our building
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What philosophers are good for...
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Short personal history
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1977
1959 - ...
2004
1989
2002
1992
1998
ECO
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European Centre for
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“Ontology”
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European Centre for
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WordNet 2.0 - 2003
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“Ontology” on the web
Popular
Ontology
Realist
The
Inactive
John
SUO
W3C
Important
most
Sowa’s
ontology
Upper
ontology
Web
from
since
citeda
August
definition:
bioinformatics
ontology
philosophical
editor
Ontology
in use.
7,from
2004.
page
Tom
Grüber
Barry
perspective.
Manchester
Initiative
initiative
resource
Smith
1993
Status Nov 29, 2004
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New search on Nov 30:
10.000 results more
What is an Ontology?
Gene Ontology Consortium
W3C Web Ontology (WebOnt) Working Group (OWL) (Closed)
Buffalo Ontology Site
MGED NETWORK :: Ontology Working Group (OWG)
Laboratory for Applied Ontology (LOA)
ONTOLOGY WORKS INC.
John Bateman; ontology portal root
The Protégé Ontology Editor and Knowledge Acquisition System
Institute for Formal Ontology and Medical Information Science ...
Autofellatio and Ontology
?????
EUROREC 2004, Implemantation Guidelines, ...
Foundational Ontology (Leeds)
Ontology Server research (StarLab)
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If, later, you can remember just one
European Centre for
Ontological Research
thing of this presentation, then
make sure it is this one:
If you use the word
“ontology”, ALWAYS
be specific about what
you mean by it.
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European Centre for
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Tom Gruber’s view
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An ontology is a specification of a
conceptualization.
The word "ontology" seems to generate a lot
of controversy in discussions about AI. It has
a long history in philosophy, in which it refers
to the subject of existence. It is also often
confused with epistemology, which is about
knowledge and knowing.
• In the context of knowledge sharing, I use the term ontology to mean
a specification of a conceptualization. That is, an ontology is a
description (like a formal specification of a program) of the concepts
and relationships that can exist for an agent or a community of
agents. This definition is consistent with the usage of ontology as
set-of-concept-definitions, but more general. And it is certainly a
different sense of the word than its use in philosophy.
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The O-word in science
N. Guarino, P. Giaretta, "Ontologies and Knowledge Bases: Towards a
Terminological Clarification". In Towards Very Large Knowledge Bases:
Knowledge Building and Knowledge Sharing, N. Mars (ed.), pp 25-32. IOS
Press, Amsterdam, 1995.
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The O-word in buzz-speak
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• “An ontology is a classification methodology for formalizing a
subject's knowledge or belief system in a structured way.
Dictionaries and encyclopedias are examples of ontologies.”
(X1)
• “A terminology (or classification) is a kind of ontology by
definition and it should preserve (and "understand") the
relationships between the 1,000s of terms in it or else it would
become a mere dictionary (or at best a thesaurus).”
(X2)
• “Ontologies are Web pages that contain a mystical unifying
force that gives differing labels common meaning.”
(X3)
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“Ontology”
An ontology defines the terms used to
describe and represent an area of
knowledge, and are used by people,
databases, and applications that need to
share domain information (a domain is a
specific subject area, such as health or
medicine). e-Health - making healthcare better for European
citizens: An action plan for a European e-Health
Area
COM
(2004) Use
356 Cases
final, 30.4.2004,
p17
OWL Web Ontology
Language;
and Requirements
W3C Recommendation 10 February 2004
http://www.w3.org/TR/webont-req/
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“Ontology”
• Ontologies need to specify descriptions for
the following kinds of concepts:
– Classes (general things) in the many domains
of interest
– The relationships that can exist among things
– The properties (or attributes) those things may
have
OWL Web Ontology Language; Use Cases and Requirements
W3C Recommendation 10 February 2004
http://www.w3.org/TR/webont-req/
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Realist Ontology
ECO
R A visit to the operating theatre
European Centre for
Ontological Research
A lot of
objects present
This
surgeon
with some relations
Part of
This mask
This
amputatio
n stump
This hand
Haydom Lutheran Hospital, Tanzania
ECO
R A visit to the operating theatre
European Centre for
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A lot of
processes going on
This wound
being closed
by holding ...
with some relations
Part of
That wound
fluid
drained
This kocher
being held in
that hand of
that surgeon
Haydom Lutheran Hospital, Tanzania
ECO
R
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“Axiom” 1
epistemology
• If the picture is not a fake, we (i.e., me and
this audience) KNOW that that hand, that
surgeon, ... EXIST(ed), i.e. ARE (were)
REAL.
• But importantly: that hand, surgeon, kocher,
mask, ... EXIST(ed) independent of our
knowledge about them and also the partrelationship between that hand and that
surgeon, and the processes going on, are
(were) equally real.
ontology
ECO
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The realist ontological
square (Ignacio Angelelli)
European Centre for
Ontological Research
Substance
Universals
instance
differentia
exemplify
Quality
Universals
instance
inheres
Substance Particulars
Quality Particulars
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R
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How to differentiate
qualities from substances ?
• Language may fool us:
– Being pale
– Being human
– Being a person
– Being sick
But so does logic:
– Pale(x)
– Human(x)
– Person(x)
– Sick(x)
• Can all be properties of particulars, namely
me and you !
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European Centre for
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“Realist ontology”
• describes what is fundamental in the totality
of what exists,
• defines the most general categories to
which we need to refer in constructing a
description of reality,
• tells us how these categories are related.
• is able to be used to describe reality at any
point in time.
ECO
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European Centre for
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Basic Ontological Notions
• Identity
– How are particulars distinguished from each
other ?
• Unity
– How are all the parts of a particular isolated ?
• Essence
– Can a property change over time ?
• Dependence
– Can an entity exist without some others ?
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Identity & instanciation
person
Living
creature
child
adult
caterpillar
butterfly
animal
t
ECO
R A practical example: OntoClean
European Centre for
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• +I
• −I
The property carries a common identity criterion for all its instances.
The property does not carry a common identity criterion for all its
instances.
• +U The property carries a common unity criterion for all its instances.
• −U The property does not carry a common unity criterion for all its
instances.
• U No instance of the property satisfies a unity criterion.
• +R The property is essential to all its instances: an instance of a rigid
property cannot stop satisfying that property.
• −R The property is not essential to all its instances: some instances of a non
rigid property can stop satisfying that property.
• R No instance of the property has it essentially: all instances of the
property can stop satisfying it.
Guarino & Welty
ECO
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Ontological theories
• = theories between reality and “the
ontology” (“ontology” as a representation)
– Granular Partition Theory (T Bittner & B. Smith)
– Logic of Classes (B. Smith)
– Foundational relations
ECO Theory of granular partitions
(B. Smith)
R
European Centre for
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Think of it as Alberti’s grid
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Granular partitions:
main principles
• a partition is the drawing of a (typically complex)
fiat boundary over a certain domain
• a partition typically comes with labels and/or an
address system
• partitions are artefacts of our cognition
• a partition is transparent (veridical)
• bona fide objects exist independently of our
partitions, fiat objects are determined by partitions
• different partitions may represent cuts through the
same reality which are skew to each other
• entities (existing in reality) located in the same cell
of a partition share common characteristics
ECO
(Simplified) Logic of classes
R
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• primitive:
– entities: particulars versus universals
– relation inst such that:
• all classes are universals; all instances are
particulars
• some particulars are not instances; e.g.
some mereological sums
• subsumption defined resorting to instances:
ECO
R
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Reference Ontology
• a theory of a domain of entities in the
world
• based on realizing the goals of maximal
expressiveness and adequacy to reality
• sacrificing computational tractability for
the sake of representational adequacy
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Basic Formal Ontology
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:
– SnapBFO, a series of snapshot ontologies (Oti ),
indexed by times: continuants
– SpanBFO a single videoscopic ontology (Ov):
occurants.
Each Oti is an inventory of all entities existing
at a time. Ov is an inventory (processory) of all
processes unfolding through time.
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Occurants and continuants
Picture by Vladimir Brajic
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SpanBFO
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“A” Realist Ontology
• a for a computer understable
representation of some pre-existing
The T-Boxreflecting
has no
domain of REALITY,
the
meaning without
be used
by its
properties of the objects
within
theto
A-Box
domain in such asoftware
way that(agents)
there obtain
• does not rely on
what
people know
or
in
a
machine,
and
substantial
and systematic correlations
think, hence no “concepts”
NOT
humans
• instance
driven,
although
it accepts itself.
between
reality
and
thebyontology
universals that are not instanciated
• does not “create” or “constrain” reality
ECO
R
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Why is the concept-based
approach so wide-spread ?
ECO
R Back to the operating theatre
European Centre for
Ontological Research
He wants
me to
remove
that blood
I must get
rid of that
blood
Suction, please !
Fluid being
removed
Haydom Lutheran Hospital, Tanzania
ECO
R
European Centre for
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This is communication !
=?
Give me a
kocher, please.
kocher
ECO
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Triadic models of meaning:
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Ontological Research
The Semiotic/Semantic triangle
Reference:
Concept / Sense / Model / View / Partition
Sign:
Language/
Term/
Symbol
Referent:
Reality/
Object
ECO
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European Centre for
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Aristotle’s triadic meaning
model
pathema
semeia

gramma/ phoné
Words spoken are signs or symbols
(symbola) of affections or impressions
(pathemata) of the soul (psyche); written
words (graphomena) are the signs of words
spoken (phoné). As writing (grammatta), so
also is speech not the same for all races of
men. But the mental affections themselves,
of which these words are primarily signs
(semeia), are the same for the whole of
mankind, as are also the objects
(pragmata) of which those affections are
representations or
likenesses, images,
copies (homoiomata).
pragma
Aristotle, 'On Interpretation', 1.16.a.4-9,
Translated by Cooke & Tredennick,
Loeb Classical Library,
William Heinemann, London, UK, 1938.
ECO
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European Centre for
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An interesting sidestep:
“understanding”
• “understanding”  Latin “substare”
– literally: “to stand under”
• Websters Dictionary (1961) understanding = the power to render
experience intelligible by bringing perceived particulars under
appropriate concepts.
• “particulars” = what is NOT SAID of a subject (Aristotle)
– substances: this patient, that tumor, ...
– qualities: the red of that patient’s skin, his body temperature,
blood pressure, ...
– processes: that incision made by that surgeon, the rise of that
patient’s temperature,...
• “concepts”: may be taken in the above definition as Aristotle’s
“universals” = what is SAID OF a subject
– Substantial concepts: patient, tumor, ...
– Quality concepts: white, temperature
– ...
ECO
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Richards’ semantic triangle
European Centre for
Ontological Research
reference
my understanding
symbol
your understanding
referent
• Reference (“concept”):
“indicates the realm of
memory where
recollections of past
experiences and
contexts occur”.
• Hence: as with Aristotle,
the reference is “mindrelated”: thought.
• But: not “the same for
all”, rather individual
mind-related
ECO
R
European Centre for
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Don’t confuse with
homonymy !
R1
R2
R3
mole (skin lesion)
mole (unit)
“mole”
mole (animal)
ECO
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European Centre for
Ontological Research
Different thoughts Homonymy
One concept
understandingof x understanding of y
R1
R2
R3
mole
“skin lesion”
mole
“unit”
symbol
referent
“mole”
mole
“animal”
ECO
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And by the way, synonymy...
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Richards’ view
the Aristotelian view
“sweat”
“perspiration”
“sweat”
“perspiration”
ECO
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Frege’s view
sense
name
• “sense” is an objective
feature of how words are
used and not a thought or
concept in somebody’s
head
• 2 names with the same
reference can have
different senses (mst/ist)
• 2 names with the same
sense have the same
reference (synonyms)
reference • a name with a sense does
not need to have a
(=referent)
reference (“Beethoven’s
10th symphony”)
ECO
R Ontology and the semantic triangle
European Centre for
Ontological Research
• In Information Science:
– “An ontology is a
description (like a formal
specification of a program)
of the concepts and
relationships that can exist
for an agent or a community
of agents.”
• In Philosophy:
– “Ontology is the science of
what is, of the kinds and
structures of objects,
properties, events,
processes and relations in
every area of reality.”
concept
term
referent
ECO
R
Current “state of the art” on
European Centre for
Ontological Research
meaning in biomedical informatics
• A pervasive bias towards “concepts”
– Content wise:
• Work based on ISO/TC37 that advocates the
Ogden-Richards theory of meaning
• Corresponds with a linguistic reading of “concept”
– Architecture wise:
• In Europe: work based on CEN/TC251 WG1 & WG2
that follow ISO/TC37
• In the US: HL7, inspired by Speech Act Theory
• “Concepts” used as elements of information models,
hence mixing a linguistic and engineering reading.
ECO
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European Centre for
Ontological Research
•
•
•
•
•
•
•
•
Before the introduction of
“concepts”, it was even worse ...
Characteristics of an ideal medical knowledge system
a unique code for each term (word, phrase)
each code-term being defined
each term independent, not defined as the result of other
terms in the system
synonyms recognisable through the codes
to each codes could be attached codes of related terms
the system would encompass all of medicine
the system would be in the public domain
the format of the KB should be functionally described,
independent from hard- or software
(C. Bishop, 1989)
ECO
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With “concepts”, it became:
European Centre for
Ontological Research
•
•
•
•
•
•
•
•
Characteristics of an ideal medical knowledge system
a unique code for each term (word, phrase) and concept
each code-term concept being defined
each term concept independent, not defined as the result
of other terms in the system
???
synonyms recognisable through the codes concepts
to each code concept could be attached codes concepts
of related terms
the system would encompass all of medicine
the system would be in the public domain
the format of the KB should be functionally described,
independent from hard- or software
ECO
Requirements for clinical
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European Centre for
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vocabularies (1)
• Domain completeness: coverage of all
possible terms that lie within a vocabulary’s
domain
• Non-vagueness: the term should represent
the concept behind it as close as possible
• Non-ambiguity: the same term cannot
refer to more than one concept
• Non-redundancy: each concept must be
represented by one unique identifier
(Cimino, 1989)
ECO
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Requirements for clinical
European Centre for
Ontological Research
vocabularies (2)
• Synonomy: multiple ways for expressing a
word (or concept) must be allowed
• Multiple classification: concepts must be
allowed to be classified in multiple
hierarchies
• Consistency of view: concepts must have
the same relationships in all views
• Explicit relationships: all relationships
(e.g. class, synonymy,…) must be explicitly
labelled.
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European Centre for
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The price you pay if you go
for concepts ...
ECO
R Border’s classification of medicine
European Centre for
Ontological Research
• Medicine
– Mental health
– Internal medicine
• Endocrinology
–Oversized endocrinology
• Gastro-enterology
• ...
– Pediatrics
– ...
– Oversized medicine
ECO
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European Centre for
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MeSH:
Medical Subject Headings
• Designed for bibliographic indexing, eg
Index Medicus
• Basis for MedLINE
• focuses on biomedicine and other basic
healthcare sciences
• clinically very impoverished
• Consistency amongst indexers:
– 60% for headings
– 30% for sub-headings
ECO
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MeSH Tree Structures - 2004
European Centre for
Ontological Research
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
Anatomy [A]
Organisms [B]
Diseases [C]
Chemicals and Drugs [D]
Analytical, Diagnostic and Therapeutic Techniques and Equipment [E]
Psychiatry and Psychology [F]
Biological Sciences [G]
Physical Sciences [H]
Anthropology, Education, Sociology and Social Phenomena [I]
Technology and Food and Beverages [J]
Humanities [K]
Information Science [L]
Persons [M]
What about this as a
Health Care [N]
top ontology ???
Geographic Locations [Z]
ECO
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MeSH Tree Structures - 2004
European Centre for
Ontological Research
• Cardiovascular Diseases [C14]
–
Heart Diseases [C14.280]
•
•
•
•
•
•
•
Arrhythmia [C14.280.067] +
Carcinoid Heart Disease [C14.280.129]
Cardiomegaly [C14.280.195] +
Endocarditis [C14.280.282] +
Heart Aneurysm [C14.280.358]
Heart Arrest [C14.280.383] +
Heart Defects, Congenital [C14.280.400]
–
–
–
–
–
–
Aortic Coarctation [C14.280.400.090]
Arrhythmogenic Right Ventricular Dysplasia [C14.280.400.145]
Cor Triatriatum [C14.280.400.200]
Coronary Vessel Anomalies [C14.280.400.210]
Crisscross Heart [C14.280.400.220]
Dextrocardia [C14.280.400.280] +
ECO
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MeSH Tree Structures - 2004
European Centre for
Ontological Research
• Body Regions [A01]
– Extremities [A01.378]
• Lower Extremity [A01.378.610]
– Buttocks [A01.378.610.100]
– Foot [A01.378.610.250]
» Ankle [A01.378.610.250.149]
» Forefoot, Human [A01.378.610.250.300] +
» Heel [A01.378.610.250.510]
– Hip [A01.378.610.400]
– Knee [A01.378.610.450]
The most abundant
– Leg [A01.378.610.500]
sort of mistakes !
– Thigh [A01.378.610.750]
ECO
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MeSH Tree Structures - 2004
European Centre for
Ontological Research
• Body Regions [A01]
–
–
–
–
Abdomen [A01.047] +
Back [A01.176] +
Breast [A01.236] +
Extremities [A01.378]
•
•
•
–
–
–
–
–
–
Amputation Stumps [A01.378.100]
Lower Extremity [A01.378.610] +
Upper Extremity [A01.378.800] +
Head [A01.456] +
Neck [A01.598]
Pelvis [A01.673] +
Perineum [A01.719]
Thorax [A01.911] +
Viscera [A01.960]
And here ?
ECO
R SNOMED International (1995)
European Centre for
Ontological Research
• Multi-axial coding system:
– morphology, disease, function, procedure, ...
• Each axis has an hierarchical structure
• Translations in other languages than English only
for older versions
• Informal internal structuring
• Being translated in CG formalism, but with only
internal consistency
• Possibility to generate meaningless concepts
• Mixing of hierarchies:
– Bone
• Long Bone
• Periosteum
• Shaft
ECO
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Snomed International (1995)
European Centre for
Ontological Research
Number of records (V3.1)
•
•
•
•
•
•
•
•
•
•
•
•
T
M
F
L
C
A
D
P
S
J
G
Topography
Morphology
Function
Living Organisms
Drugs &Biological Products
Physical Agents, Forces and Activities
Disease/ Diagnosis
Procedures
Social Context
Occupations
General Modifiers
TOTAL RECORDS
12,385
4,991
16,352
24,265
14,075
1,355
28,623
27,033
433
1,886
1,176
132,641
ECO
R Snomed International (1995):
European Centre for
Ontological Research
knowledge in the codes.
T
-
3
5
3
2
2
posterior
anatomic
leaflet
mitral
cardiac valve
cardiovascular
Why was this not a good idea ?
ECO
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Snomed International :
multiple ways to express the same thing
European Centre for
Ontological Research
D5-46210
Acute appendicitis, NOS
D5-46100
G-A231
Appendicitis, NOS
Acute
M-41000
G-C006
T-59200
Acute inflammation, NOS
In
Appendix, NOS
G-A231
M-40000
G-C006
T-59200
Acute
Inflammation, NOS
In
Appendix, NOS
ECO
R The International Classification
European Centre for
Ontological Research
•
•
•
•
•
•
•
•
•
•
•
•
•
•
•
of diseases (WHO).
...
Chapter II:
Neoplasms (C00-D48)
Chapter III:
Diseases of the Blood and Blood-forming organs and certain
disorders involving the immune mechanism (D50-D89)
Excludes :
auto-immune disease (systemic) NOS (M35.9)
....
Nutritional Anemias (D50-D53)
D50 Iron deficiency anaemia
Includes: ...
D50.0 Iron deficiency anaemia secondary to blood loss (chronic)
Excludes : ...
D50.1
...
D51 Vit B12 deficiency anaemia
Haemolytic Anemias (D55-D59)
...
Chapter IV: ...
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European Centre for
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UMLS: Unified Medical
Language System (NLM)
• Tool for information retrieval of 4 components:
– Metathesaurus contains information about biomedical
concepts and how they are represented in diverse
terminological systems.
– Semantic Network contains information about concept
categories and the permissible relationships among
them
– Information Sources Map contains both humanreadable and machine-processable information about
all kinds of biomedical terminological systems
– Specialist lexicon: english words with POS
• “The” tool from and for the U.S.
:-)
ECO UMLS Semantic Network
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European Centre for
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ECO
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European Centre for
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•
•
•
•
•
•
Semantic Network
Relationships
Is_a
physically related to
spatially related to
temporally related to
functionally related to
conceptually related to
ECO
Semantic Network “Biologic
R
Function” Hierarchy
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Semantic Network
"affects" Hierarchy
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“Axiom” 2
• Concept-based terminology (and standardisation
thereof) is there as a mechanism to improve
understanding of messages by humans.
• It is NOT the right device
– to explain why reality is what it is, how it is organised,
etc., (although it is needed to allow communication),
– to reason about reality,
– to make machines understand what is real,
– to integrate across different views, languages,
conceptualisations, ...
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European Centre for
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Why not ?
• Does not take care of universals and particulars
appropriately
• Concepts not necessarily correspond to
something that (will) exist(ed)
– Sorcerer, unicorn, leprechaun, ...
• Definitions set the conditions under which terms
may be used, and may not be abused as
conditions an entity must satisfy to be what it is
• Language can make strings of words look as if it
were terms
– “Middle lobe of left lung”
• ...
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European Centre for
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Ok, then Description Logics
will save us ... ?
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European Centre for
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Description Logics
• A decidable fragment of FOL
• A propositional modal logic
• A classes and properties (concepts and roles)
oriented KR language
• Subsumption and satisfiability (consistency) are
the key inferences
• Most DLs are supersets of ALC
– Boolean operators on concepts
– Existential and Universal quantifiers
• OWL-DL is a large superset (SHOIN):
–
–
–
–
Property hierarchies & Transitive roles (SH)
Inverse (I)
Nominals (O) (hasValue and one of)
Number restrictions (counting quantifiers)
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European Centre for
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Snomed and DL
SNOMED-RT (2000)
SNOMED-CT (2003)
DL don’t guarantee you to get parthood right !
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Use of description logics does not
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guarantee correct representations !
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Sloppiness in definitions
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new-1
new-2
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European Centre for
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NCI Thesaurus
• a biomedical thesaurus created
specifically to meet the needs of the
National Cancer Institute.
• semantically modeled cancer-related
terminology built using description
logics
ECO
R NCI Thesaurus Root concepts
European Centre for
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Anatomic
Or
? Does Substance
Structure,
the NCI not
Anatomic
? know
If yes,towhy
System,
which
is gene
category
or
Anatomic
Any
product
itemnot
classified
Substance
subsumed
there
?by belongs
it ? If no,? why are
drugs and chemicals not subsumed by it ?
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European Centre for
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Conceptual entity
• Definition: none
• Semantic type:
– Conceptual entity
– Classification
• Subconcepts:
– Action:
• definition: action; a thing done
– And:
• Definition: an article which expresses the relation of
connection or addition, used to conjoin a word with a word, ...
– Classification
• Definition: the grouping of things into classes or categories
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Definition of “cancer gene”
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NCI Thesaurus architecture
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Findings-AndDisorders-Kind
Anatomy-Kind
What diseases have a diameter of over 3 cm ?
Disease
ISA
“Kinds”
“Associative”
“Formal
restrict the
relationships
subsumption”
domain andproviding
range
or of
associative
“inheritance”
“differentiae”
relationships
Breast neoplasm
Breast
Disease-has-associated-anatomy
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European Centre for
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Ontology versus
Description Logics
• In the Description Logic world
– terms and definitions come first,
– the job is to validate them and reason with them by
means of a model
– but whether the model correspond to reality is not its
problem (Workshop on DL, Saarbrücken, 22-23/11/2004)
• In the realist ontology world
– robust ontology (with all its reasoning power) comes
first
– terms, term-hierarchies and record architectures must
be subjected to the constraints of ontological
coherence
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Thanks x there is OWL ?
Where x  {
,
,
}
,
,
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Understanding content (1)
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“John Doe has a pyogenic
granuloma of the left thumb”
John Doe has a
pyogenic
granuloma of
the left thumb
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Understanding content (2)
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<record>
<patient>John Doe</patient>
<diagnosis>pyogenic granuloma of the left thumb</diagnosis>
</record>
<record>
<subject> John Doe </subject>
<diagnosis> pyogenic granuloma
of the left thumb </diagnosis>
</record>
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Understanding content (3)
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<129465004>
<116154003>John Doe</116154003>
< 8319008 > 17372009
<finding site> 76505004
<laterality>7771000</laterality>
</finding site>
</ 8319008 >
</129465004>
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European Centre for
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XML
OWL
• XML
– Pure syntax
– Simulated semantics
• OWL:
– Very precise semantics
– But is the semantics of the right sort to faithfully
describe simple medical facts ?
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NCIT’s “Lung” in OWL
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<owl:Class rdf:ID="Lung">
<rdfs:label>Lung</rdfs:label> “All instances of lung must be
located in at least one instance
<code>C12468</code>
of thoracic cavity”
<hasType>primitive</hasType>
Hence: total lung excision is
<rdfs:subClassOf rdf:resource="#Organ"/>
impossible.
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty
rdf:resource="#rAnatomic_Structure_Has_Location"/>
<owl:someValuesFrom rdf:resource="#Thoracic_Cavity"/>
</owl:Restriction>
</rdfs:subClassOf>
...
</owl>
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NCIT’s “Lung” in OWL
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<owl:Class rdf:ID="Lung">
“every assigned location of
<rdfs:label>Lung</rdfs:label>
pleura must be an instance of
<code>C12468</code>
the class Thoracic Cavity”
<hasType>primitive</hasType>
Allows lungs not to be located
<rdfs:subClassOf rdf:resource="#Organ"/>
at all.
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty
rdf:resource="#rAnatomic_Structure_Has_Location"/>
<owl:allValuesFrom rdf:resource="#Thoracic_Cavity"/>
</owl:Restriction>
</rdfs:subClassOf>
...
</owl>
ECO
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European Centre for
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Take home messages
• Very few “ontologies” are ontologies.
• Realist ontology offers a good methodology
for building consistent representations.
• DLs are helpful, but only if you know how to
use them properly.
• OWL is inadequate to represent even the
most obvious facts.
• Please ... be critical when buzz words are
used.