In research often only the unspeakable is worth saying.
Werner Ceusters
Biomedical Natural Language Understanding:
Adopting Ontological Realism as the Next Step
July 16, 2010
Lister Hill Center building (Blg 38A), NIH, Bethesda, MD
Prof. Werner CEUSTERS, MD
Ontology Research Group, Center of Excellence in Bioinformatics and Life Sciences
and
Department of Psychiatry, University at Buffalo, NY, USA
In research often only the unspeakable is worth saying.
Werner Ceusters
?
1977
1959
-
2010
2006
Short personal
history
1989
2004
1992
2002
1995
1993
1998
In research often only the unspeakable is worth saying.
Werner Ceusters
Context: CgSB research
• Builds and improves systems that extract biomedical
information from free text
• Seeks to determine the accessibility and understandability
of health information
• Develops systems to help users retrieve and integrate
electronic biomedical information
• Investigates all aspects of creating and disseminating
digital library collections
• Tests theories to enhance or improve current research and
development activities
In research often only the unspeakable is worth saying.
Werner Ceusters
A trajectory of mixes and mingles …
Informatics
Electronic
Health Records
Medicine
Knowledge Representation
In research often only the unspeakable is worth saying.
Werner Ceusters
Education and Training
Informatics
Knowledge Representation
• MD, Board certified (in Belgium)
– neuro-psychiatry (last of its kind)
– healthcare informatics
• PostDoctoral Degree (~MSc)
– knowledge engineering (Dept. of philosophy)
Electronic
Health Records
Medicine
• theoretical parts focused on epistemology, philosophy of
language, modal and non-monotonic logics, fuzzy
logics,
• practical parts: design of problem-specific representation
languages
• Awards from the Belgian and Dutch Medical
Informatics Organizations on computer-based
patient (and provider) assessment instrument
In research often only the unspeakable is worth saying.
Werner Ceusters
Missionary work through EU funded projects
• MEDIREC  PROREC:
1994
– Getting EHR systems accepted nationally
– Promoting quality criteria for data capture and data
exchange
• EUROREC:
2000
2010
– European alignment of EHR systems
– Certification of EHR systems
• ARGOS: Transatlantic Observatory for Meeting
Global Health Policy Challenges through ICT-Enabled
Solutions
– includes AMIA
In research often only the unspeakable is worth saying.
Werner Ceusters
A trajectory of mixes and mingles … (2)
Knowledge Representation
Informatics
Linguistics
Computational Linguistics
Medical Natural
Language Understanding
Electronic
Health Records
Medicine
In research often only the unspeakable is worth saying.
Werner Ceusters
My interest in NLU: prove the 1990 HIT dogma wrong
• Fact: computers can only deal with a structured
representation of reality:
– structured data:
• relational databases, spread sheets
– structured information:
• XML simulates context
– structured knowledge:
• rule-based knowledge systems
• Conclusion: a need for structured data entry
?
In research often only the unspeakable is worth saying.
Werner Ceusters
Structured data entry
• Prevailing technical solutions:
– rigid data entry forms
– coding and classification systems
• But:
– the description of biological variability requires the
flexibility of natural language and it is generally
desirable not to interfere with the traditional manner of
medical recording (Wiederhold, 1980)
– Initiatives to facilitate the entry of narrative data have
focused on the control rather than the ease of data
entry (Tanghe, 1997)
In research often only the unspeakable is worth saying.
Werner Ceusters
Drawbacks of structured data entry
• Loss of information
– qualitatively
• limited expressiveness of coding and classification systems,
controlled vocabularies, and “traditional” medical
terminologies
• use of purpose oriented systems
– don’t use data for another purpose than originally foreseen
– quantitatively
• to time-consuming to code all information manually
• Speech recognition and structured data entry forms
are not best friends
In research often only the unspeakable is worth saying.
Werner Ceusters
Early research in EU funded projects
• ANTHEM: automatic coding of diagnostic
•
•
•
•
expressions in ICD-10
Multi-Tale: syntactic – semantic tagging
of terms and phrases in surgery reports
– collaboration with Naomi Sager
DOME: Document Management in
Healthcare Informatics Systems.
– collaboration with Pierre Zweigenbaum
GALEN-IN-USE: development of a large scale
medical terminologic knowledge base.
ToMeLo: building a Strategic Alliance between
Developers of Medical Terminology and Health Care
Record Systems
In research often only the unspeakable is worth saying.
Werner Ceusters
MultiTale: synsem - tagging
Dura was incised in linear fashion and the scar around the inlet of the reservoir
was dissected out until the ventricular catheter was exposed and withdrawn
under direct vision.
<Clause type="surg">
<Segment role="do" semtype="anat" syntax="sg" meaning="T-A1120">Dura
</Segment>
<Segment role="action" semtype="open" syntax="papa" meaning="P101000">
<SegConst.1 syntax="past">was </SegConst.1>
<SegConst.1 role="action" semtype="open" syntax="papa" meaning="P101000">incised </SegConst.1></Segment>
<Segment syntax="prep">in </Segment>
<Segment semtype="manner" syntax="adjnoun" meaning="(G-A148,G-D430)">
<SegConst.1 semtype="mod" syntax="adj" meaning="G-A148">linear
</SegConst.1>
<SegConst.1 semtype="manner" syntax="sg" meaning="G-D430">fashion
</SegConst.1></Segment>
</Clause>
In research often only the unspeakable is worth saying.
Lexical, semantic and ontological relations
Werner Ceusters
urine
gall bladder
gallbladder
inflammation
bladder
urinary bladder
inflammation
bile
urinary
bladder
‘urinary’
inflammation
‘biliary cystitis’
‘cystitis’
‘gallbladder
’
‘urinary
bladder’
‘inflammation’
‘bladder’
‘gallbladder
inflammation’
‘urinary bladder
inflammation’
In research often only the unspeakable is worth saying.
Werner Ceusters
MultiTale in GALEN-IN-USE
The Galen view
ResourseManagementProcess
InstallingProcess
LiquidInstallingProcess
Filling
Injecting
The linguistic semantic view
To install <theme> [ in <goal> ]
To fill
<goal> [with <theme> ]
To inject <theme> [ in <goal> ]
To inject <goal>
In research often only the unspeakable is worth saying.
Werner Ceusters
Cassandra-II: from LR to CR
({valgising}5(osteotomy)1{[of]3(humerus)2}4)22
((cutting)21
{[TO_ACHIEVE]6((Deed:valgising)7
{[ACTS_ON]17(Pathology:pathologicalposture)18}19)20}5
{[ACTS_ON]3(Anatomy:humerus)2}4)22
In research often only the unspeakable is worth saying.
Werner Ceusters
Language & Computing nv / Inc.
• Created in 1998 with traditional 3F investors, raised $10,000,000
capital in 2000
• Mission: develop NLU applications to turn medical free text into
structured representations
• I functioned as CTO and VP R&D until 2004
– my team: 12 MDs, 4 computational linguists, 5 software engineers
• Several awards:
– 1998: startup company of the year Flanders Technology International
– 2003: Frost and Sullivan Healthcare Information Technology and Life
Sciences Product-of-the-Year Award
• Patent accepted in 2009
• Bought by Nuance Inc (“Dragon”) in 2010
In research often only the unspeakable is worth saying.
Werner Ceusters
Client applications
• Coding patient data
• Structured information extraction from
unstructured clinical notes
• Checking clinical protocols and guidelines
• Assessing patient eligibility for clinical trial entry
• Generate triggers and alerts
• Linking case descriptions to scientific literature
• Easy access to content
• ... towards a medical semantic web
In research often only the unspeakable is worth saying.
Werner Ceusters
NLU patent filed in 2001, accepted in 2009
In research often only the unspeakable is worth saying.
Werner Ceusters
My 1998 requirements for NLU
1. Knowledge about terms and how they are used in valid
constructions within natural language;
2. Knowledge about the world, i.e. how the referents
denoted by the terms interrelate in reality and in given
types of context;
3. An algorithm that is able to calculate a language user’s
representation of that part of the world described in the
utterances that are the subject of the analysis.
In research often only the unspeakable is worth saying.
Werner Ceusters
Not easy: e.g. ambiguous phrasings
warning on plastic bag
in Amsterdam hotel elevator
in Miami hotel lobby
In research often only the unspeakable is worth saying.
Werner Ceusters
Understanding content (1)
We see:
“John Doe has a pyogenic
granuloma of the left thumb”
The machine sees:
John Doe has a
pyogenic
granuloma of
the left thumb
In research often only the unspeakable is worth saying.
Werner Ceusters
Understanding content (2)
We see:
The XML misunderstanding
<record>
<patient>John Doe</patient>
<diagnosis>pyogenic granuloma of the left thumb</diagnosis>
</record>
The machine sees:
<record>
<subject> John Doe </subject>
<diagnosis> pyogenic granuloma
of the left thumb </diagnosis>
</record>
In research often only the unspeakable is worth saying.
Werner Ceusters
The clever (?) business man and his XML card
<business-card>
<name> John Nitwit </name>
Is this the name of the business card
<address>
or of the business card owner?
<street> 524 Moon base avenue </street>
<city> Utopia </city>
</address>
<phone> … </phone>
…
</business-card>
In research often only the unspeakable is worth saying.
Werner Ceusters
Exploit the relationships along the vertices
Halliday’s systemic
functional
grammar
The structures of language are
partially determined by our
conceptualisation of the
world.
Halliday
No mental representation
without language Fodor
Aristotelian
realism
concept
Meaning is located in
the interaction between living
beings and the environment
language
James J. Gibson, Ecological
Realism in Psychology
referents
Baboons and humans have different cut-off points for discerning "same" objects because
our verbal expression for "same" makes the idea of "same" more restrictive.”
Fagot and Wasserman (Centre for Research in Cognitive Neuroscience in Marseille)
In research often only the unspeakable is worth saying.
Werner Ceusters
Halliday’s systemic functional grammar
• A “complete” theory for NLU
– constructivistic basis: “language construes human
experience”
– English: It is raining
– Chinese: The sky drops water
• hence: natural languages are instances of generic schemes
– macro-structure of documents
• derive a “structural formula”
– micro-structure of documents
• lexical cohesion
• in-conjunction analysis
In research often only the unspeakable is worth saying.
Werner Ceusters
L&C’s LinkFactory
Language A
Proprietary Terminologies
Language
LexiconB
Lexicon
Others ...
Grammar
ICPC
Grammar
SNOMED
Formal Domain
Ontology
ICD
Linguistic Ontology
MEDRA
In research often only the unspeakable is worth saying.
Use of spatial logics
Werner Ceusters
HASOVERLAPPING
-REGION
HASPARTIALSPATIALOVERLAP
ISSPATIAL
-PARTOF
ISPROPERSPAT.PART-OF
HAS-DISCRETEDREGION
HASSPATIAL
-PART
HASPROPERSPATIAL
-PART
HAS-SPATIALPOINTREFERENCE
HASCONNECTINGREGION
HASDISCONNECTEDREGION
HASEXTERNALIS-NONCONNECTINGTANG.ISREGION
SPAT.TANG.IS- HAS-NON- HASPART-OF
SPAT.- SPAT.- TANG.- TANG.PART-OF EQUIV.- SPAT.SPAT.OF
PART
PART
ISIS-PARTLYIN-CONVEX- INSIDECONVEXISHULL-OF
HULL-OF
OUTSIDECONVEXHULL-OF
ISIS-GEOINSIDE- TOPOINSIDEOF
OF
In research often only the unspeakable is worth saying.
Werner Ceusters
Example: (canonical) joint anatomy
• joint HAS-HOLE joint space
• joint capsule IS-OUTER-LAYER-OF joint
• meniscus
– IS-INCOMPLETE-FILLER-OF joint space
– IS-TOPO-INSIDE joint capsule
– IS-NON-TANGENTIAL-MATERIAL-PART-OF
joint
• joint
– IS-CONNECTOR-OF bone X
– IS-CONNECTOR-OF bone Y
• synovia
– IS-INCOMPLETE-FILLER-OF joint space
• synovial membrane IS-BONAFIDEBOUNDARY-OF joint space
In research often only the unspeakable is worth saying.
Werner Ceusters
Gap Finder and Web Agent
In research often only the unspeakable is worth saying.
Werner Ceusters
In research often only the unspeakable is worth saying.
Werner Ceusters
In research often only the unspeakable is worth saying.
Werner Ceusters
In research often only the unspeakable is worth saying.
Werner Ceusters
In research often only the unspeakable is worth saying.
Werner Ceusters
In research often only the unspeakable is worth saying.
Werner Ceusters
In research often only the unspeakable is worth saying.
Werner Ceusters
A trajectory of mixes and mingles …(3)
Knowledge Representation
Informatics
Linguistics
Computational Linguistics
Medical Natural
Language Understanding
Electronic
Health Records
Medicine
Ontology
Philosophy
Realism-Based
Ontology
In research often only the unspeakable is worth saying.
Werner Ceusters
The two faces of ‘ontology’
• In philosophy:
– Ontology (no plural) is the study of what entities
exist and how they relate to each other;
• In mainstream computer science and
biomedical informatics:
– An ontology (plural: ontologies) is a shared and
agreed upon conceptualization of a domain;
– usually: a terminology in disguise
In research often only the unspeakable is worth saying.
Werner Ceusters
Few embrace both and they should be applauded
• ‘A message to mapmakers:
highways are not painted
red, rivers don't have
county lines running down
the middle, and you can't
see contour lines on a
mountain.’
Bill Kent
1936-2005
William Kent, Data and Reality. First published by North Holland in 1978.
Republished in 1998 by 1stBooks.
In research often only the unspeakable is worth saying.
Werner Ceusters
MeSH: Geographic Locations [Z01]
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Africa [Z01.058] +
Americas [Z01.107] +
Antarctic Regions [Z01.158]
Arctic Regions [Z01.208]
Asia [Z01.252] +
Atlantic Islands [Z01.295] +
Australia [Z01.338] +
Cities [Z01.433] +
Europe [Z01.542] +
Historical Geographic Locations
[Z01.586] +
Indian Ocean Islands [Z01.600] +
Oceania [Z01.678] +
Oceans and Seas [Z01.756] +
Pacific Islands [Z01.782] +
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Ancient Lands [Z01.586.035] +
Austria-Hungary [Z01.586.117]
Commonwealth of Independent States
[Z01.586.200] +
Czechoslovakia [Z01.586.250] +
European Union [Z01.586.300]
Germany [Z01.586.315] +
Korea [Z01.586.407]
Middle East [Z01.586.500] +
New Guinea [Z01.586.650]
Ottoman Empire [Z01.586.687]
Prussia [Z01.586.725]
Russia (Pre-1917) [Z01.586.800]
USSR [Z01.586.950] +
Yugoslavia [Z01.586.980] +
In research often only the unspeakable is worth saying.
Werner Ceusters
MeSH hierarchies
All MeSH Categories
???
Diseases Category
Nervous System Diseases
Male Urogenital
Diseases
Eye Diseases
Cranial Nerve
Diseases
Optic Nerve
Diseases
Eye Diseases,
Hereditary
has
…
Optic Nerve
Diseases
Optic Atrophy
Female Urogenital Diseases
and Pregnancy Complications
Female Urogenital Diseases
Neurodegenerative
Diseases
Heredodegenerative
Disorders,
Nervous System
Urologic Diseases
Kidney Diseases
Optic Atrophies,
Hereditary
has
Wolfram
Syndrome
Diabetes Insipidus
In research often only the unspeakable is worth saying.
Werner Ceusters
Terminological versus Ontological approach
• The terminologist defines:
– ‘a clinical drug is a pharmaceutical product given to (or taken
by) a patient with a therapeutic or diagnostic intent’. (RxNorm)
• The (good, real) ontologist thinks:
– Does ‘given’ includes ‘prescribed’?
– Is manufactured with the intent to … not sufficient?
• Are newly marketed products – available in the pharmacy, but not yet
prescribed – not clinical drugs?
• Are products stolen from a pharmacy not clinical drugs?
• What about such products taken by persons that are not patients?
– e.g. children mistaking tablets for candies.
In research often only the unspeakable is worth saying.
Werner Ceusters
This dichotomy is also present in simple words
Solving crimes through Referent Tracking
Huey Pierce Long, Jr.
Carl Austin Weiss, MD
(Aug 30, 1893 - Sept 10, 1935)
(Dec 6, 1906 – Sept 8, 1935)
In research often only the unspeakable is worth saying.
Werner Ceusters
A double mystery
•
On September 9th, 1935, Carl Austin Weiss
shot Senator Huey Long in the Louisiana State Capitol
with a .35 calibre pistol. Long died from this wound thirty
hours later on September 10th. Weiss, on the other hand,
received between thirty-two and sixty .44 and .45 calibre
hollow point bullets from Long's agitated bodyguards and
died immediately.
(It is argued that)
Sorensen, R., 1985, "Self-Deception and Scattered Events", Mind, 94: 64-69.
• Questions:
– Did Weiss kill Senator Long ?
– If so, when did he kill him ?
In research often only the unspeakable is worth saying.
Werner Ceusters
What this demonstrates
• What things are and how things are named, are
two different issues,
• (Natural) language does not fit nicely with reality,
– formed at a time when insight in reality was crippled,
– did not evolve accurately enough with our insight,
• Human brains have the capacity not to be bothered
too much by the unfaithfulness of natural
language.
In research often only the unspeakable is worth saying.
Werner Ceusters
Computers lack this ability
• Knowledge representation and semantic
interoperability are for machines, not humans;
• Computer languages and knowledge
representations must at least be unambiguous, and
preferably also faithful to (our best understanding of)
reality.
• Unfortunately, the majority of them don’t precisely
because of the confusion between terminology and
ontology.
In research often only the unspeakable is worth saying.
Werner Ceusters
My 2004 requirements for NLU
1.
Knowledge about terms and how they are used in valid
constructions within natural language;
2. Knowledge about the world, i.e. how the referents denoted by the
terms interrelate in reality and in given types of context;
3. An algorithm that :
a. is able to calculate a language user’s representation of that part
of the world described in the utterances that are the subject of
the analysis.
b. can track the ways in which people express what does NOT
represent anything in reality (eg for medico-legal reasons)
Only a realist ontology (and not an ontology that deals with
“alternative realities”) permits correct disambiguation
between 3a and 3b.
In research often only the unspeakable is worth saying.
Werner Ceusters
Basic axioms of philosophical realism
1. There is an external reality which
is ‘objectively’ the way it is;
2. That reality is accessible to us;
3. We build in our brains cognitive
representations of reality;
4. We communicate with others
about what is there, and what we
believe there is there.
Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the
Biomedical Domain. Proceedings of KR-MED 2006, Biomedical Ontology in Action, November 8, 2006, Baltimore MD, USA
In research often only the unspeakable is worth saying.
Werner Ceusters
Compare with Alberti’s grid
Ontological
theory
representation
reality
In research often only the unspeakable is worth saying.
Werner Ceusters
No serious scholar should work with ‘concepts’
In research often only the unspeakable is worth saying.
Werner Ceusters
Slow penetration of the idea …
In research often only the unspeakable is worth saying.
Werner Ceusters
More serious scholars become convinced …
what is a concept
description a
description of?
In research often only the unspeakable is worth saying.
Werner Ceusters
but Kantians will never …
In research often only the unspeakable is worth saying.
Werner Ceusters
Observations and similarities
In research often only the unspeakable is worth saying.
Werner Ceusters
Observations and similarities
Are these pictures of concepts or of horses ?
Is this a sensible question:
‘What concepts have tails and do …?’
In research often only the unspeakable is worth saying.
Werner Ceusters
Observations and similarities
Are these pictures of concepts?
If concepts are in brains, that must be
awfully big brains!
Are these pictures of anything at all?
In research often only the unspeakable is worth saying.
Werner Ceusters
And confusion is thus everywhere
in terminologies, classifications and ‘ontologies’
• SNOMED:
– ‘Disorders are concepts in which there is an explicit or
implicit pathological process causing a state of disease
which tends to exist for a significant length of time
under ordinary circumstances.’
– And also: “Concepts are unique units of thought”.
– Thus: Disorders are unique units of thoughts in
which there is a pathological process …???
– And thus: to eradicate all diseases in the world at once
we simply should stop thinking ?
In research often only the unspeakable is worth saying.
Werner Ceusters
Diagnosis versus disease
The diagnosis is here
The disease is there
In research often only the unspeakable is worth saying.
Werner Ceusters
A trajectory of mixes and mingles … (4)
Knowledge Representation
Informatics
Linguistics
Computational Linguistics
Medical Natural
Language Understanding
Electronic
Health Records
Medicine
Ontology
Philosophy
Realism-Based
Ontology
Referent
Tracking
In research often only the unspeakable is worth saying.
Werner Ceusters
Terminologies for ‘unambiguous representation’ ???
PtID
Date
ObsCode
Narrative
5572
04/07/1990
26442006
closed fracture of shaft of femur
5572
04/07/1990
81134009
Fracture, closed, spiral
5572
12/07/1990
26442006
closed fracture of shaft of femur
5572
12/07/1990
9001224
Accident in public building (supermarket)
5572
04/07/1990
79001
Essential hypertension
0939
24/12/1991
255174002
benign polyp of biliary tract
2309
21/03/1992
26442006
closed fracture of shaft of femur
2309
21/03/1992
9001224
Accident in public building (supermarket)
47804
03/04/1993
58298795
Other lesion on other specified region
5572
17/05/1993
79001
Essential hypertension
298
22/08/1993
2909872
Closed fracture of radial head
298
22/08/1993
9001224
Accident in public building (supermarket)
5572
01/04/1997
26442006
closed fracture of shaft of femur
5572
01/04/1997
79001
Essential hypertension
0939
20/12/1998
255087006
malignant polyp of biliary tract
In research often only the unspeakable is worth saying.
Werner Ceusters
The problem in a nutshell
• Generic terms used to denote specific entities do not have
enough referential capacity
– Usually enough to convey that some specific entity is denoted,
– Not enough to be clear about which one in particular.
• For many ‘important’ entities, unique identifiers are used:
–
–
–
–
UPS parcels
Patients in hospitals
VINs on cars
…
In research often only the unspeakable is worth saying.
Werner Ceusters
Fundamental goals of ‘our’ Referent Tracking
explicit reference to the
concrete individual entities
relevant to the accurate
description of some
portion of reality, ...
Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health Records.
J Biomed Inform. 2006 Jun;39(3):362-78.
In research often only the unspeakable is worth saying.
Werner Ceusters
Method: numbers instead of words
– Introduce an Instance
Unique Identifier (IUI)
for each relevant
particular (individual)
entity
78
Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health Records.
J Biomed Inform. 2006 Jun;39(3):362-78.
In research often only the unspeakable is worth saying.
Werner Ceusters
Codes for ‘types’ AND identifiers for instances
PtID
Date
ObsCode
Narrative
5572
04/07/1990
26442006
IUI-001
closed fracture of shaft of femur
5572
04/07/1990
81134009
IUI-001
Fracture, closed, spiral
5572
12/07/1990
26442006
IUI-001
closed fracture of shaft of femur
5572
12/07/1990
9001224
IUI-007
Accident in public building (supermarket)
5572
04/07/1990
79001
IUI-005
Essential hypertension
0939
24/12/1991
255174002
IUI-004
benign polyp of biliary tract
2309
21/03/1992
26442006
IUI-002
closed fracture of shaft of femur
2309
21/03/1992
9001224
IUI-007
Accident in public building (supermarket)
47804
03/04/1993
58298795
IUI-006
Other lesion on other specified region
5572
17/05/1993
79001
IUI-005
Essential hypertension
298
22/08/1993
2909872
IUI-003
Closed fracture of radial head
298
22/08/1993
9001224
IUI-007
Accident in public building (supermarket)
5572
01/04/1997
26442006
IUI-012
closed fracture of shaft of femur
5572
01/04/1997
79001
IUI-005
Essential hypertension
IUI-004
malignant polyp of biliary tract
0939
20/12/1998
255087006
7 distinct
disorders
In research often only the unspeakable is worth saying.
Werner Ceusters
The problem of reference in free text
• ‘The surgeon examined Maria. She found a small
tumor on the left side of her liver. She had it
removed three weeks later.’
• Ambiguities:
–
–
–
–
who denotes the first ‘she’: the surgeon or Maria ?
on whose liver was the tumor found ?
who denotes the second ‘she’: the surgeon or Maria ?
what was removed: the tumor or the liver ?
• Here referent tracking can come to aid.
In research often only the unspeakable is worth saying.
Werner Ceusters
Fundamental goals of ‘our’ Referent Tracking
Use these identifiers in expressions using a language that
acknowledges the structure of reality:
e.g.: a yellow ball:
then not : yellow(#1) and ball(#1)
rather: #1: the ball
#2: #1’s yellow
Then still not:
ball(#1) and yellow(#2) and hascolor(#1, #2)
but rather:
instance-of(#1, ball, since t1) Strong foundations
instance-of(#2, yellow, since t2) in realism-based
inheres-in(#1, #2, since t2)
ontology
In research often only the unspeakable is worth saying.
Werner Ceusters
The shift envisioned
• From:
– ‘this person is a 40 year old patient with a stomach tumor’
• To (something like):
– ‘this-1 on which depend this-2 and this-3 has this-4’, where
•
•
•
•
•
•
•
•
•
•
this-1
this-2
this-2
this-3
this-3
this-4
this-4
this-5
this-5
…
instanceOf
instanceOf
qualityOf
instanceOf
roleOf
instanceOf
partOf
instanceOf
partOf
human being …
age-of-40-years …
this-1 …
patient-role …
this-1 …
tumor …
this-5 …
stomach …
this-1 …
In research often only the unspeakable is worth saying.
Werner Ceusters
The shift envisioned
• From:
– ‘this man is a 40 year old patient with a stomach tumor’
• To (something like):
– ‘this-1 on which depend this-2 and this-3 has this-4’, where
•
•
•
•
•
•
•
•
•
•
this-1
this-2
this-2
this-3
this-3
this-4
this-4
this-5
this-5
…
instanceOf
instanceOf
qualityOf
instanceOf
roleOf
instanceOf
partOf
instanceOf
partOf
human being …
age-of-40-years …
this-1 …
patient-role …
this-1 …
tumor …
this-5 …
stomach …
this-1 …
denotators for particulars
In research often only the unspeakable is worth saying.
Werner Ceusters
The shift envisioned
• From:
– ‘this man is a 40 year old patient with a stomach tumor’
• To (something like):
– ‘this-1 on which depend this-2 and this-3 has this-4’, where
•
•
•
•
•
•
•
•
•
•
this-1
this-2
this-2
this-3
this-3
this-4
this-4
this-5
this-5
…
instanceOf
instanceOf
qualityOf
instanceOf
roleOf
instanceOf
partOf
instanceOf
partOf
human being …
age-of-40-years …
this-1 …
patient-role …
this-1 …
tumor …
this-5 …
stomach …
this-1 …
denotators for appropriate relations
In research often only the unspeakable is worth saying.
Werner Ceusters
The shift envisioned
• From:
– ‘this man is a 40 year old patient with a stomach tumor’
• To (something like):
– ‘this-1 on which depend this-2 and this-3 has this-4’, where
•
•
•
•
•
•
•
•
•
•
this-1
this-2
this-2
this-3
this-3
this-4
this-4
this-5
this-5
…
instanceOf
instanceOf
qualityOf
instanceOf
roleOf
instanceOf
partOf
instanceOf
partOf
human being
age-of-40-years
this-1
patient-role
this-1
tumor
this-5
stomach
this-1
…
…
…
…
…
…
…
denotators
for universals
…
… or particulars
In research often only the unspeakable is worth saying.
Werner Ceusters
The shift envisioned
• From:
– ‘this man is a 40 year old patient with a stomach tumor’
• To (something like):
– ‘this-1 on which depend this-2 and this-3 has this-4’, where
•
•
•
•
•
•
•
•
•
•
this-1
this-2
this-2
this-3
this-3
this-4
this-4
this-5
this-5
…
instanceOf
instanceOf
qualityOf
instanceOf
roleOf
instanceOf
partOf
instanceOf
partOf
human being
age-of-40-years
this-1
patient-role
this-1
tumor
this-5
stomach
this-1
…
…
…
…
…
…
…
…
…
time stamp in
case of
continuants
In research often only the unspeakable is worth saying.
Werner Ceusters
Relevance: the way RT-compatible systems ought to interact
with representations of generic portions of reality
instance-of at t
caused
#105
by
In research often only the unspeakable is worth saying.
Werner Ceusters
‘Principles for Success’
• Evolutionary change
• Radical change:
• Principle 6: Architect Information and Workflow Systems to
Accommodate Disruptive Change
» Organizations should architect health care IT for flexibility to
support disruptive change rather than to optimize today’s ideas
about health care.
• Principle 7: Archive Data for Subsequent Re-interpretation
» Vendors of health care IT should provide the capability of
recording any data collected in their measured, uninterpreted,
original form, archiving them as long as possible to enable
subsequent retrospective views and analyses of those data.NOTE
Willam W. Stead and Herbert S. Lin, editors; Committee on Engaging the Computer Science
Research Community in Health Care Informatics; National Research Council. Computational
Technology for Effective Health Care: Immediate Steps and Strategic Directions (2009)
In research often only the unspeakable is worth saying.
Werner Ceusters
A trajectory of mixes and mingles …
Knowledge Representation
Informatics
Linguistics
Computational Linguistics
Medical Natural
Language Understanding
Electronic
Health Records
Translational
Research
Medicine
Biology
Ontology
Philosophy
Realism-Based
Ontology
Referent
Tracking
Pharmacogenomics
Pharmacology
Performing
Arts
Defense &
Intelligence
In research often only the unspeakable is worth saying.
Werner Ceusters
Semantic Interoperability (SI)
the ability of two or more computer systems to
exchange information in such a way that the
meaning of that information can be automatically
interpreted by the receiving system accurately
enough to produce useful results to the end users of
both systems.
In research often only the unspeakable is worth saying.
Werner Ceusters
‘Full interoperability’
• ‘Neither language nor technological differences
prevent the system to seamlessly integrate the
received information into the local record and
provide a complete picture of someone’s health as
if it would have been collected locally.’
• ‘Further, the anonymized data feeds directly into
the tools of public health authorities and
researchers.’
Stroetmann et.al. Semantic Interoperability for Better Health and Safer Healthcare. SemabticHEALTH report. Jan 2009
In research often only the unspeakable is worth saying.
Werner Ceusters
And meaning is, of course, the problem
• ‘I know that you believe that you understood
what you think I said, but I am not sure you
realize that what you heard is not what I meant.’
– Robert McCloskey, State Department spokesman
(attributed).
• http://www.quotationspage.com/quotes/Robert_McCloskey/
In research often only the unspeakable is worth saying.
Werner Ceusters
Current Research
• Revision of the appropriatness of concept-based
terminology for specific purposes;
• Relationship between models and that part of
reality that the models want to represent;
• Adequacy of current tools and languages for
representation;
• Boundaries between terminology and ontology
and the place of each in semantic interoperability;
• Apply this in natural language understanding.
In research often only the unspeakable is worth saying.
Terminology component
Werner Ceusters
uses
0..
term
*
assessment
instrument
source
used-for
1..
part-of 1
term in
context
part-of
1..
*
has-part
1
uses
1..
*
expressed-by
meaning
0..1
expresses
broader
1..*
narrower
0..*
corresponds-to
0..*
uses
* used-for
used-for
dataset 1..
*
*
1
data
element
0..*
bridging axiom
uses
dataset
ontology
1
uses
instrument
ontology
0..* used-for
1
uses
application ontology
representational
element
ontology
Ontology component
used-for
*
used-in
1..
1..
1 means
1..
Data component
0..*
has-part 0..*
0..*
data
dictionary
*
used-for 1..
*
uses
0..*
representational
unit
1..
*
reference ontology
In research often only the unspeakable is worth saying.
Werner Ceusters
?
1977
1959
-
2010
2006
Short personal
history
1989
2004
1992
2002
1995
1993
1998
In research often only the unspeakable is worth saying.
Werner Ceusters
?
1977
1959
-
2030?
2006
Short personal
history
1989
2004
1992
2002
1995
1993
1998
In research often only the unspeakable is worth saying.
Werner Ceusters
Sometimes being ugly pays off …
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