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ECOREuropean Centre forOntological Research
European Developmentsin Realist Ontology.
Dr. Werner Ceusters, MDExecutive Director
European Centre for Ontological ResearchSaarland University
Saarbrücken, Germany
ECOREuropean Centre forOntological Research
Main message
You’d better start first with ontology !
If you are not an ontologist, try to marry one.
ECOREuropean Centre forOntological Research
Funded Ontology-basedNLP research projects
Dome‘94 - ‘95
GIU‘96 - ‘99
Anthem‘93 - ‘96
MultiTale‘93 - ‘96
ToMeLo‘97 - ‘99
Select‘98 – ‘00
Liquid‘01 – ‘03
Homey‘01 – ‘04
SCOP‘02 – ‘05
FF-Poirot‘02 – ‘05
O
t
ECOREuropean Centre forOntological Research
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={lex=ouvrir}& ({lemma=ouvrir,head={AVOIR,ehead={sem={EVENT}}}} ;{lemma=ouvreur,head={CNT,ehead={MASC,sem={NOPROF}}}} ;{lemma=ouvreuse,head={CNT,ehead={FEM,sem={NOPROF}}}} ;{lemma=ouvert,head={ADJ_POST,ehead={sem={STATE}}}} ;{lemma=ouvertement,head={ADV,ehead={sem={EVENT}}}} ;{lemma=ouverture, head={CNT,ehead={FEM,sem=({APERTURE};{EVENT})}}})& {sc={a={AGENT},b={THEME}}}
ECOREuropean Centre forOntological Research
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
ECOREuropean Centre forOntological Research
DO DO
IO
IO M DO IO M
SURGICAL DEED
SURGICAL
PROCEDURE
INTERVENTIONAL EQUIPMENT
PATHOLOGY HUMAN
ANATOMY
CEN ENV1828: Model of surgical procedures.
DO: Direct ObjectIO: Indirect ObjectM: Means
ECOREuropean Centre forOntological Research SNOMED-RT CT
• Concept-based medical terminology
ECOREuropean Centre forOntological Research
Triadic models of meaning: The Semiotic/Semantic triangle
Sign:Language/
Term/Symbol
Referent:Reality/Object
Reference: Concept / Sense / Model / View
ECOREuropean Centre forOntological Research
MultiTALE’s sentence analysis
action repair noun closed reduction > P1-10E30 - - prep of do path sg fracture of zygoma or
zygomatic arch - path sg fracture of zygoma - path sg fracture > M-12000 - - prep of - anat sg zygoma > T-11168 - - coor or - anat adjnoun zygomatic arch > T-11167
“closed reduction of fracture of zygoma or zygomatic arch”
ECOREuropean Centre forOntological Research
DOME: XML-representation of Medical DOcuments
<?XML version="1.0" ?><?XML:stylesheet type="text/XSL" href="cr-radio.xsl" ?><CR-RADIOLOGIE><ENTETE> <INFORMATION-SERVICE> <HOPITAL>Groupe hospitalier Léonard Devintscie</HOPITAL> <SERVICE>Radiologie Centrale</SERVICE><MEDECIN>Dr. Bouaud</MEDECIN> <TITRE-EXAMEN>Phlébographie des membres inférieurs</TITRE-EXAMEN> </INFORMATION-SERVICE> <INFORMATION-DEMANDE> <SERVICE>Sce Pr. Charlet</SERVICE><MEDECIN>Dr. Brunie</MEDECIN> <DATE>29-10-99</DATE> </INFORMATION-DEMANDE> <INFORMATION-PATIENT ID="236784020"><NOM>Donald</NOM> <PRENOM>Duck</PRENOM></INFORMATION-PATIENT></ENTETE> <BODY> <INDICATION>Suspicion de phlébite de jambe gauche</INDICATION> <TECHNIQUE>Ponction bilatérale d’une veine du dos du pied et injection de 180cc de produit de contraste</TECHNIQUE> <RESULTATS>image lacunaire endoluminale visible au niveau des veines péronières gauche. Absence d’opacification des veines tibiales antérieures et postérieures gauches. Les veines illiaques et la veine cave inférieure sont libres. </RESULTATS> <CONCLUSION>Trombophlébite péronière et probablement tibiale antérieure et postérieure gauche.</CONCLUSION> </BODY></CR-RADIOLOGIE>
ECOREuropean Centre forOntological Research 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 Pen&Pad.
ECOREuropean Centre forOntological Research
• 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”
The GALEN-IN-USE Project
(SurgicalDeed which isMainlyCharacterisedBy (performance whichG isEnactmentOf ((Incising which playsClinicalRole SurgicalRole) whichG < hasSpecificGoal ( (Valgising which playsClinicalRole SurgicalRole) whichG LocativeAttribute PathologicStandingPosture) actsSpecificallyOn Humerus>)))
ECOREuropean Centre forOntological Research Give more depth to the flat
surgical procedure model
closed reduction fracture zygoma zygomatic arch
accessmethod repair
body structure separation
bone containing body region
modifiersurgical
procedure pathology anatomy
concept
HAS APPROACH
ACTS ONHAS LOCATION
ECOREuropean Centre forOntological Research
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
ECOREuropean Centre forOntological Research 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 Deed:valgising
ACTS_ON Pathology:pathological posture
ACTS_ON Anatomy: humerus
ECOREuropean Centre forOntological Research
Need for a “linguistic ontology”
The Galen view The linguistic semantic view
ResourseManagementProcess InstallingProcess To install <theme> [ in <goal> ] LiquidInstallingProcess Filling To fill <goal> [with <theme> ] Injecting To inject <theme> [ in <goal> ]
To inject <goal>
ECOREuropean Centre forOntological Research
(excision)35 {[of]111 ((cicatrix)2120 {[of]216 (skin)474}0)0}0(debridement)82 {[of]142 ({palmar}1785 (skin)474)0}0
RefId Prototype Conceptual repr. Linguistic repr.
35 excision excising excising82 debridement debriding debriding111 of ACTS_ON THEME142 of ACTS_ON SOURCE216 of HAS_LOCATION SOURCE474 skin skin skin1785 palmar IS_PART_OF(palm) LOCATIVE(palm)
2120 cicatrix cicatrix cicatrix
Building bridges
ECOREuropean Centre forOntological Research
Rule based model conversion
Conceptual Linguistic
representation representation
excising excising
ACTS_ON cicatrix THEME cicatrix
HAS_LOC skin SOURCE skin
ECOREuropean Centre forOntological Research
SCOP
Ontology Query
ECOREuropean Centre forOntological Research
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
ECOREuropean Centre forOntological Research Ontology based parsing
ONTOLOGY
PatientIs-possessor-of
Cancer patient
IS-A
Has-Healthcare-phenomenon
2
2
IS-A
3
3
Having a healthcare phenomenon
Healthcare phenomenon
IS-A
Has-possessor Has-
possessed
Malignant neoplasm
IS-A
11
1
IS-A
IS-A
Mr. Smith has a pulmonary carcinoma
Generalised PossessionHuman
lung carcinoma
1. Parsing2. Relating
3. Inferring
Mr. Smith has a pulmonary carcinoma
ECOREuropean Centre forOntological Research
A “statistics only system”
22 page full paper
ABSTRACT ONLY
ECOREuropean Centre forOntological Research Relative Concept/Node
identification (real)
0
0,05
0,1
0,15
0,2
0,25
0,3
0,35
0,4
0 500 1000 1500 2000 2500 3000 3500 4000 4500 5000
Nr of words
concepts
nodes
ECOREuropean Centre forOntological Research
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.”
concept
term referent
definition
concept
term referent
definition
ECOREuropean Centre forOntological Research
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.
ECOREuropean Centre forOntological Research
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.: +49 (0)681-302-64770 Fax: +49 (0)681-302-64772
ECOREuropean Centre forOntological Research
IFOMIS’s long-term goal
• Build a robust high-level BFO-MedO framework
• THE WORLD’S FIRST INDUSTRIAL-STRENGTH PHILOSOPHY
• which can serve as the basis for an ontologically coherent unification of medical knowledge and terminology
ECOREuropean Centre forOntological Research
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, ...
ECOREuropean Centre forOntological Research
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
ECOREuropean Centre forOntological Research
European Centrefor
Ontological Research
ECOREuropean Centre forOntological Research
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
ECOREuropean Centre forOntological Research
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
ECOREuropean Centre forOntological Research
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.
ECOREuropean Centre forOntological Research Affiliations and Partners
ECOREuropean Centre forOntological Research Management
Directors Representatives of affiliates
AdvisoryBoard
Strategic Management Board
ECOREuropean Centre forOntological Research 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
ECOREuropean Centre forOntological Research
Financing
• European research grants
• Industrial partner program
• Consultancy
ECOREuropean Centre forOntological Research
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
ECOREuropean Centre forOntological Research
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.
ECOREuropean Centre forOntological Research
Tools and resources for systems-level interpretation of diseases:
Understanding diabetes as a complex disease
• Network of Excellence– Streamlining research– Tools sharing
ECOREuropean Centre forOntological Research
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
ECOREuropean Centre forOntological Research
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