Presentation is loading. Please wait.

Presentation is loading. Please wait.

ECO R European Centre for Ontological Research European Developments in Realist Ontology. Dr. Werner Ceusters, MD Executive Director European Centre for.

Similar presentations


Presentation on theme: "ECO R European Centre for Ontological Research European Developments in Realist Ontology. Dr. Werner Ceusters, MD Executive Director European Centre for."— Presentation transcript:

1 ECO R European Centre for Ontological Research European Developments in Realist Ontology. Dr. Werner Ceusters, MD Executive Director European Centre for Ontological Research Saarland University Saarbrücken, Germany

2 ECO R European Centre for Ontological Research Main message You’d better start first with ontology ! If you are not an ontologist, try to marry one.

3 ECO R European Centre for Ontological Research Funded Ontology-based NLP 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

4 ECO R European Centre for Ontological 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}}}

5 ECO R European Centre for Ontological 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

6 ECO R European Centre for Ontological 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 Object IO: Indirect Object M: Means

7 ECO R European Centre for Ontological Research SNOMED-RT  CT Concept- based medical terminology

8 ECO R European Centre for Ontological Research Triadic models of meaning: The Semiotic/Semantic triangle Sign: Language/ Term/ Symbol Referent: Reality/ Object Reference: Concept / Sense / Model / View

9 ECO R European Centre for Ontological 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”

10 ECO R European Centre for Ontological Research DOME: XML-representation of Medical DOcuments Groupe hospitalier Léonard Devintscie Radiologie Centrale Dr. Bouaud Phlébographie des membres inférieurs Sce Pr. Charlet Dr. Brunie 29-10-99 Donald Duck Suspicion de phlébite de jambe gauche Ponction bilatérale d’une veine du dos du pied et injection de 180cc de produit de contraste 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. Trombophlébite péronière et probablement tibiale antérieure et postérieure gauche.

11 ECO R European Centre for Ontological 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.

12 ECO R European Centre for Ontological 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>))) 

13 ECO R European Centre for Ontological Research Give more depth to the flat surgical procedure model closedreductionfracturezygomazygomatic arch access method repair body structure separation bone containing body region modifier surgical procedure pathologyanatomy concept HAS APPROACH ACTS ON HAS LOCATION

14 ECO R European Centre for Ontological 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

15 ECO R European Centre for Ontological 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

16 ECO R European Centre for Ontological Research Need for a “linguistic ontology” The Galen view The linguistic semantic view ResourseManagementProcess InstallingProcess To install [ in ] LiquidInstallingProcess Filling To fill [with ] Injecting To inject [ in ] To inject

17 ECO R European Centre for Ontological 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 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 Building bridges

18 ECO R European Centre for Ontological Research Rule based model conversion Conceptual Linguistic representation representation excising excising ACTS_ON cicatrixTHEME cicatrix HAS_LOC skinSOURCE skin

19 ECO R European Centre for Ontological Research SCOP Ontology Query

20 ECO R European Centre for Ontological 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

21 ECO R European Centre for Ontological Research Ontology based parsing ONTOLOGY Patient Is-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 1 1 1 Mr. Smith has a pulmonary carcinoma Generalised Possession Human lung carcinoma 1. Parsing 2. Relating 3. Inferring Mr. Smith has a pulmonary carcinoma

22 ECO R European Centre for Ontological Research A “statistics only system” 22 page full paper ABSTRACT ONLY

23 ECO R European Centre for Ontological Research Relative Concept/Node identification (real) concepts nodes

24 ECO R European Centre for Ontological 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.”

25 ECO R European Centre for Ontological Research Why are concepts not 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.

26 ECO R European Centre for Ontological 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

27 ECO R European Centre for Ontological 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

28 ECO R European Centre for Ontological Research IFOMIS’ research in Formal Ontology Formal treatment of universals, individuals, endurants, perdurants, scales, functions, collections,... Universals / Concepts Meriology and topology Vagueness and granularity Applicability to domain ontologies, terminologies,...

29 ECO R European Centre for Ontological 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

30 ECO R European Centre for Ontological Research European Centre for Ontological Research

31 ECO R 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

32 ECO R European Centre for Ontological 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

33 ECO R European Centre for Ontological 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.

34 ECO R European Centre for Ontological Research Affiliations and Partners

35 ECO R European Centre for Ontological Research Management Directors Representatives of affiliates Advisory Board Strategic Management Board

36 ECO R European Centre for Ontological 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

37 ECO R European Centre for Ontological Research Financing European research grants Industrial partner program Consultancy

38 ECO R European Centre for Ontological 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

39 ECO R European Centre for Ontological 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.

40 ECO R European Centre for Ontological Research Tools and resources for systems- level interpretation of diseases: Understanding diabetes as a complex disease Network of Excellence – Streamlining research – Tools sharing

41 ECO R European Centre for Ontological 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

42 ECO R European Centre for Ontological 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


Download ppt "ECO R European Centre for Ontological Research European Developments in Realist Ontology. Dr. Werner Ceusters, MD Executive Director European Centre for."

Similar presentations


Ads by Google