European Developments in Realist Ontology.

European Developmentsin Realist Ontology. Dr. Werner Ceusters, MD Executive Director European Centre for Ontological Research Saarland 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 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

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

SURGICAL DEED DO DO SURGICAL HUMAN PATHOLOGY IO PROCEDURE ANATOMY IO M DO IO M INTERVENTIONAL EQUIPMENT CEN ENV1828: Model of surgical procedures. DO: Direct Object IO: Indirect Object M: Means

SNOMED-RT  CT • Concept-based medical terminology

Triadic models of meaning: The Semiotic/Semantic triangle Reference: Concept / Sense / Model / View Sign: Language/ Term/ Symbol Referent: Reality/ Object

MultiTALE’s sentence analysis “closed reduction of fracture of zygoma or zygomatic arch” 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

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 niveaudes veines péronières gauche. Absence d’opacificationdes 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>

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.

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”  (SurgicalDeedwhichisMainlyCharacterisedBy (performancewhichGisEnactmentOf ((IncisingwhichplaysClinicalRoleSurgicalRole) whichG <hasSpecificGoal ( (ValgisingwhichplaysClinicalRoleSurgicalRole) whichGLocativeAttributePathologicStandingPosture) actsSpecificallyOnHumerus>)))

concept surgical procedure modifier pathology anatomy HASAPPROACH bone containing body region body structure separation access method repair ACTSON HASLOCATION closed reduction fracture zygoma zygomatic arch Give more depth to the flat surgical procedure model

The Galen view: linguistic knowledge conceptual knowledge pragmatic knowledge criteria knowledge terminological knowledge Clean separation of knowledge • The L.E. view: • phonologic knowledge • morphologic knowledge • syntactic knowledge • semantic knowledge • pragmatic knowledge • world knowledge

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 viewThe 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>

Building bridges (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 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

Rule based model conversion Conceptual Linguistic representation representation excising excising ACTS_ON cicatrix THEME cicatrix HAS_LOC skin SOURCE skin

Ontology Query SCOP

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

Generalised Possession Healthcare phenomenon Human Has- possessor Has- possessed IS-A 1 1 2 1 IS-A Having a healthcare phenomenon IS-A 2 Is-possessor-of Patient Has-Healthcare-phenomenon Malignant neoplasm IS-A 3 IS-A 3 ONTOLOGY Cancer patient lung carcinoma IS-A Ontology based parsing 1. Parsing 2. Relating 3. Inferring Mr. Smithhasa pulmonary carcinoma Mr. Smith has a pulmonary carcinoma

22 page full paper ABSTRACT ONLY A “statistics only system”

Relative Concept/Node identification (real) 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.”

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 SecretariatTel.: +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 Centre for 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.

Affiliations and Partners

Management Strategic Management Board Advisory Board Directors Representatives of affiliates

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

European Developments in Realist Ontology.