European Developments in Realist Ontology.

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European Developmentsin Realist Ontology.

• Dr. Werner Ceusters, MD
• Executive Director
• European Centre for Ontological Research
• Saarland University
• Saarbrücken, Germany

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Main message

• Youd better start first with ontology !

If you are not an ontologist, try to marry one.
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Funded Ontology-basedNLP research projects
O
SCOP 02 05
GIU 96 - 99
Homey 01 04
FF-Poirot 02 05
ToMeLo 97 - 99
Liquid 01 03
MultiTale 93 - 96
Select 98 00
Dome 94 - 95
Anthem 93 - 96
t
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ANTHEM

• Advanced Natural Language Interface for
  Multilingual Text Generation in Healthcare
• Semantic features used to
• Restrict the hypothesis space of sentence
  interpretations
• Build semantic representation of a sentence
• Build translation / coded statement according to
  provisions of medical classification system

ouvrir lexouvrir (lemmaouvrir,headAVOIR,
eheadsemEVENT lemmaouvreur,headCNT,e
headMASC,semNOPROF lemmaouvreuse,head
CNT,eheadFEM,semNOPROF
lemmaouvert,headADJ_POST,eheadsemSTATE
lemmaouvertement,headADV,eheadsemEVENT
lemmaouverture, headCNT,eheadFE
M,sem(APERTUREEVENT))
scaAGENT,bTHEME
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Multi-TALE

• The generation of MULTI-lingual specialised
  lexicons by using augmented TAgger-LEmmatizers.
• Two objectives
• Generate semantic lexicons on the basis of
  surgical procedure reports, through the glasses
  of CEN ENV 1828 and SNOMED-RT
• Analyse new texts to derive a structured
  representation of each action described,
  according to CEN ENV 1828 and SNOMED-RT

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CEN ENV1828 Model of surgical procedures.
DO Direct Object IO Indirect Object M Means
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SNOMED-RT ? CT

• Concept-based medical terminology

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Triadic models of meaning The Semiotic/Semantic
triangle
Reference Concept / Sense / Model / View
Sign Language/ Term/ Symbol
Referent Reality/ Object
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MultiTALEs sentence analysis
closed reduction of fracture of zygoma or
zygomatic arch
action repair noun closed reduction gt
P1-10E30 - - prep of do path
sg fracture of zygoma or
zygomatic arch - path sg
fracture of zygoma - path sg
fracture gt M-12000 - - prep
of - anat sg zygoma gt
T-11168 - - coor or -
anat adjnoun zygomatic arch gt T-11167
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DOME XML-representation of Medical DOcuments
lt?XML version"1.0" ?gt lt?XMLstylesheet
type"text/XSL" href"cr-radio.xsl"
?gt ltCR-RADIOLOGIEgtltENTETEgt ltINFORMATION-SERVICEgt
ltHOPITALgtGroupe hospitalier Léonard
Devintscielt/HOPITALgt ltSERVICEgtRadiologie
Centralelt/SERVICEgtltMEDECINgtDr. Bouaudlt/MEDECINgt
ltTITRE-EXAMENgtPhlébographie des membres
inférieurslt/TITRE-EXAMENgt lt/INFORMATION-SERVICEgt
ltINFORMATION-DEMANDEgt ltSERVICEgtSce Pr.
Charletlt/SERVICEgtltMEDECINgtDr. Brunielt/MEDECINgt
ltDATEgt29-10-99lt/DATEgt lt/INFORMATION-DEMANDEgt
ltINFORMATION-PATIENT ID"236784020"gtltNOMgtDonaldlt/
NOMgt ltPRENOMgtDucklt/PRENOMgtlt/INFORMATION-PAT
IENTgtlt/ENTETEgt ltBODYgt ltINDICATIONgtSuspicion
de phlébite de jambe gauchelt/INDICATIONgt
ltTECHNIQUEgtPonction bilatérale dune veine du dos
du pied et injection de 180cc de produit
de contrastelt/TECHNIQUEgt ltRESULTATSgtimage
lacunaire endoluminale visible au niveau des
veines péronières gauche. Absence dopacification
des veines tibiales antérieures et postérieures
gauches. Les veines illiaques et la veine cave
inférieure sont libres. lt/RESULTATSgt
ltCONCLUSIONgtTrombophlébite péronière et
probablement tibiale antérieure et
postérieure gauche.lt/CONCLUSION
gt lt/BODYgt lt/CR-RADIOLOGIEgt
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GALEN

• Generalised Architecture for Languages,
  Encyclopaedias and Nomenclatures in Medicine
• The GRAIL-language a description logic for
  representing medical knowledge
• The CORE a steadily growing model of medicine
  written in GRAIL
• (One of) the first serious ontology projects in
  healthcare grown out of PenPad.

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The GALEN-IN-USE Project

• building a model of surgical procedures
• distributed collaborate modeling in various
  modeling centers
• dissections as intermediate representation
• Our task to populate the GALEN ontology
  semi-automatically
• valgising incision of humerus

?
(SurgicalDeed which isMainlyCharacterisedBy
(performance whichG isEnactmentOf
((Incising which playsClinicalRole SurgicalRole)
whichG lt hasSpecificGoal
( (Valgising which
playsClinicalRole SurgicalRole)
whichG LocativeAttribute
PathologicStandingPosture)
actsSpecificallyOn
Humerusgt)))
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Give more depth to the flat surgical procedure
model
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Clean separation of knowledge

• The Galen view
• linguistic knowledge
• conceptual knowledge
• pragmatic knowledge
• criteria knowledge
• terminological knowledge

• The L.E. view
• phonologic knowledge
• morphologic knowledge
• syntactic knowledge
• semantic knowledge
• pragmatic knowledge
• world knowledge

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From language to dissections to GRAIL

• RUBRIC valgiserende osteotomie van humerus
• ENGLISH_RUBRIC "valgising osteotomy of humerus"
• PARAPHRASE "osteotomy of humerus with purpose to
  create a valgising position"
• SOURCE "WCC"
• CODE "5-781.21"
• MAIN cutting
• TO_ACHIEVE Deedvalgising
• ACTS_ON Pathologypathological posture
• ACTS_ON Anatomy humerus

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Need for a linguistic ontology
The Galen view The linguistic
semantic view ResourseManagementProcess
InstallingProcess To install ltthemegt in
ltgoalgt LiquidInstallingProcess
Filling To fill ltgoalgt with ltthemegt
Injecting To inject
ltthemegt in ltgoalgt To inject
ltgoalgt
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Building bridges

• (excision)35 of111 ((cicatrix)2120 of216
  (skin)4740)00
• (debridement)82 of142 (palmar1785
  (skin)474)00
• RefId Prototype Conceptual repr.
  Linguistic repr.
• 35 excision excising excising
• 82 debridement debriding debriding
• 111 of ACTS_ON THEME
• 142 of ACTS_ON SOURCE
• 216 of HAS_LOCATION SOURCE
• 474 skin skin skin
• 1785 palmar IS_PART_OF(palm)
  LOCATIVE(palm)
• 2120 cicatrix cicatrix cicatrix

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Rule based model conversion

• Conceptual Linguistic
• representation representation
• excising excising
• ACTS_ON cicatrix THEME cicatrix
• HAS_LOC skin SOURCE skin

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SCOP
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FF-Poirot

• Building an ontology to detect and fight
  Financial Fraud
• Electronic invoicing
• VAT regulations
• Internet advertisements for financial services
  with fraudulous character
• Intended
• Non-intended

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Ontology based parsing
1. Parsing
2. Relating
3. Inferring
Mr. Smith has a pulmonary carcinoma
Mr. Smith has a pulmonary carcinoma
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A statistics only system
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Relative Concept/Node identification (real)
concepts
nodes
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Lessons learned

• Ontology 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.
• Ontology 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.

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Why are conceptsnot enough?

• Why must our theory address also the referents in
  reality?
• Because referents are observable fixed points in
  relation to which we can work out how the
  concepts used by different communities relate to
  each other
• Because only by looking at referents can we
  establish the degree to which concepts are good
  for their purpose.

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IFOMIS Institute for Formal Ontology and
Medical Information Science
The Institute for Formal Ontology and Medical
Information Science was founded in April 2002 as
part of the Faculty of Medicine of the University
of Leipzig utilizing a grant of the Alexander von
Humboldt Foundation. It comprehends an
interdisciplinary research group with members
from Philosophy, Computer and Information
Science, Logic, Medicine, and Medical
Informatics. IFOMIS established itself as a
center of theoretically grounded research in both
formal and applied ontology. Its goal is to
develop a formal ontology that will be applied
and tested in the domain of medical and
biomedical information science. In August 2004
IFOMIS moved its base of operations from Leipzig
to Saarland University in Saarbrücken.
IFOMIS Universität des Saarlandes Postfach
151150 D-66041 Saarbrücken Germany
Secretariat Tel. [phone] Fax
49 (0)681-302-64772
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IFOMISs long-term goal

• Build a robust high-level BFO-MedO framework
• THE WORLDS FIRST INDUSTRIAL-STRENGTH PHILOSOPHY
• which can serve as the basis for an ontologically
  coherent unification of medical knowledge and
  terminology

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IFOMIS research inFormal Ontology

• Formal treatment of universals, individuals,
  endurants, perdurants, scales, functions,
  collections, ...
• Universals / Concepts
• Meriology and topology
• Vagueness and granularity
• Applicability to domain ontologies,
  terminologies, ...

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IFOMIS successes

• Identification of mistakes in concept-based
  terminologies
• SNOMED-CT
• LinkBase
• Convincing developers of such systems to adopt a
  more principled approach
• Gene Ontology
• Foundational Medical Anatomy

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European Centre for Ontological Research
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Objectives

• a new approach in applying ontology to a variety
  of problems in information science and related
  areas
• advocates a vision in which careful attention is
  paid to what the world is like to which an
  ontology-based system is to be applied
• draw on the expertise and skills of existing
  institutions throughout Europe

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Network of Affiliates and Partners

• ECOR Affiliates have ontology as their primary
  focus of research
• ECOR Partners bring a range of different types of
  expertise related either to
• horizontal areas
• software engineering,
• formal reasoning,
• language technology,
• vertical domains
• bio-informatics,
• finance,
• law

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Principle-based approach

• ECOR does not dictate any particular
  philosophical or metaphysical stance with respect
  to reality.
• the very same reality may be sliced in different
  ways when addressed from different perspectives.
• The approach requires however that, whatever
  philosophical stance is taken, it is used
  consistently and rigourously and on the basis of
  clearly stated principles.

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Affiliations and Partners
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Management
Strategic Management Board
Advisory Board
Directors
Representatives of affiliates
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Industrial partners program

• possibility of proposing new high priority
  research topics
• notification of research proposals and invitation
  to join relevant consortia
• personalised consultancy designed to show how
  ontology can be applied in a commercial
  environment
• training in ontology tailored to the needs of a
  specific business
• participation in publications, conferences and
  workshops
• dissemination of results and of services
• notification of upcoming events

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Financing

• European research grants
• Industrial partner program
• Consultancy

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European Research Grants

• 6th FP ... 7th FP
• Well-defined objectives and areas of research
• Various types of actions
• Integrated Projects
• Networks of Excellence
• Accompanying measures
• Cross-border collaboration
• Intra-EU
• United States

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LIFESCIHEALTH Life sciences, genomics and
biotechnology for health

• Development of a European-wide package for
  creating and integrating relevant databases and
  analysis software to enable systems-level
  interpretation of complex experimental data in
  functional genomics.
• Fundamental knowledge and basic tools for
  functional genomics in all organisms
• The strategic objective of this line is to foster
  the basic understanding of genomic information,
  by developing the knowledge base, tools and
  resources needed to decipher the function of
  genes and gene products relevant to human health
  and to explore their interactions with each other
  and with their environment.
• Bioinformatics
• enable researchers to access efficient tools for
  managing and interpreting the ever-increasing
  quantities of genome data and for making it
  available to the research community in an
  accessible and usable form.

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Tools and resources for systems-level
interpretation of diseases Understanding
diabetes as a complex disease

• Network of Excellence
• Streamlining research
• Tools sharing

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Clinical bioinformatics project for the 10 most
common male and female cancers in Europe

• EBI
• Swiss Prot people
• University Hospital of Geneva and Satellites
• Roswell Park very welcome

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Implementations in the US

• BCOR
• Buffalo Centre of Ontological Research
• NCOR
• National Centre of Ontological Research
• Stanford University (Mark Musen)
• Setup, objectives, management, ... discussion
  for this afternoon