ECO R European Centre for Ontological Research European Developments in Realist Ontology. Dr. Werner...

ECOREuropean Centre forOntological Research

European Developmentsin Realist Ontology.

Dr. Werner Ceusters, MDExecutive Director

European Centre for Ontological ResearchSaarland University

Saarbrücken, Germany


Main message

You’d better start first with ontology !

If you are not an ontologist, try to marry one.


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


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}}}


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


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


Triadic models of meaning: The Semiotic/Semantic triangle

Sign:Language/

Term/Symbol

Referent:Reality/Object

Reference: Concept / Sense / Model / View


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”


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.


• 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


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


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>


(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


Rule based model conversion

Conceptual Linguistic

representation representation

excising excising

ACTS_ON cicatrix THEME cicatrix

HAS_LOC skin SOURCE skin


SCOP

Ontology Query


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


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


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


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.


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


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


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, ...


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


European Centrefor

Ontological 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


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


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


Financing

• European research grants

• Industrial partner program

• Consultancy


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


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.


Tools and resources for systems-level interpretation of diseases:

Understanding diabetes as a complex disease

• Network of Excellence– Streamlining research– Tools sharing


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


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

ECO R European Centre for Ontological Research European Developments in Realist Ontology. Dr. Werner...

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