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GOL A General Ontological Language

GOL A General Ontological Language. Wolfgang Degen Inst. of Theoretical Informatics University of Erlangen. Barbara Heller Inst. of Medical Informatics University of Leipzig. Heinrich Herre Inst. of Medical Informatics University of Leipzig. Barry Smith Department of Philosophy

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GOL A General Ontological Language

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  1. GOLA General Ontological Language Wolfgang Degen Inst. of Theoretical Informatics University of Erlangen Barbara Heller Inst. of Medical Informatics University of Leipzig Heinrich Herre Inst. of Medical Informatics University of Leipzig Barry Smith Department of Philosophy University of Buffalo

  2. Contents • Aims and Motivation • Application Scenario • Sets, Individuals, Universals • Basic Types of Individuals • Basic Types of Relations • Comparison to Upper-Level Ontologies • Future Research

  3. Aims of the Project GOL • Development of a well-founded upper-level ontology • Construction of a unified framework for modelling ontological structures • Applications to the medical domain Application Scenario

  4. Application scenario: Competence Network for Malignant Lymphomas • About 10,000 new diseases a year • Great therapeutic progress • Different established clinical trial groups • Hodgkin-Lymphomas • High-malignant Non-Hodgkin-Lymphomas • Low-malignant Non-Hodgkin-Lymphomas with over 30 clinical trial protocols with up to 300 clinics/practitioners with different reference centres for diagnosis and therapy

  5. Application oriented Goal of GOL Definition of ontologically based biometrical and medical data dicitionaries in the field of protocol- and guideline- based medicine is essential for Realisation of a computer-based quality management in clinical trial execution • based on the harmonization of documentation criteria • predefinition of processes for controlling and securing data and process quality

  6. Information and Communication Services based on Data Dictionaries Participants Clinics, Oncol. Specialists Primary Pathologists Radio Therapists Self-help Groups Patients & Relatives Material Data Input Requests Acknowledgement I N T E R N E T Depositions Documents Participants‘ Specific Query Notification Documentation Judgement Notification Information Services Clinical Trial Centres Reference Centres Morbus Hodgkin Hm-NHL Lm-NHL Heterogenous Data Bases Data Dictionaries Reference-RX Reference-Pathology Reference-Laboratories Heterogenous Data Bases Communication Services Data Bases Patient Data Patient Data Electonical dispatch Material dispatch (conventional)

  7. Motivation I • Every domain-specific ontology must use some upper-level ontology • Standard modelling languages such as KIF, CycL, F-logic are confined to set-theoretical construction principles • Standard classification systems in medicine such as GALEN, UMLS, SNOMED are not strong enough

  8. Motivation II ClaimThere are ontological relations between urelements (objects, things, events ...) which exist independently of set-theoretical structures. We want to work with the real things directly; not with set- theoretical substitutes

  9. Ontology versus Set Theory The facile translation of ontological relations into sets removes the possibility of our gaining insight into reality

  10. Hierarchy of Categories Top-Category Entity Relation Set Urelement formal material Universal Individual Substance Moment Chronoid Topoid Situoid

  11. Hierarchy of Universals Universals Substrate Space Time Colour Shape . . . solid fluid gas

  12. Sets and Urelements I Sets • abstract entities • independent of space and time • determined by their extensions Urelements • not sets • have internal structure which the membership relation cannot unfold

  13. Sets and Urelements II Basic Axiom For every finite collection of entities there exists a set containing them as elements

  14. Individuals and Universals I Individuals • belong to the realm of concrete things • are confined by space and time Universals • abstract entities • independent of space and time • determined by their intensions • are patterns of features realized by their instances

  15. Individuals and Universals II Basic Axiom • For every universal U there exists a set S which is the extension Ext(U) of U • Ext(U) = { a : a is instance of U}

  16. Substances • exists in and of itself • possesses material bulk • occupies space • bears qualities Examples you and me, the moon, a tennis ball, a house, a desk

  17. Moments • can exist only in a substance • are dynamic • can be lost over time Examplesactions, passions, a blush, a handshake, a thought

  18. Situoids I • are parts of the world that can be comprehended as a whole and do not need other entities in order to exist • always imply a certain cut through reality, which means: a certain granularity and point of view

  19. Situoids II • each situoid has associated with it a finite number of universals, which are (roughly) those universals which we need in order to grasp the situoid itself • the universals associated with a situoid determine which material relations and individuals occur in it and thus which granularity and viewpoint it presupposes

  20. Situoids III • have a location in space and time • frame a certain spatial region (called a topoid) and a certain temporal interval (called a chronoid)

  21. Situoids IV Examples 1 • Johns kissing of Mary in a certain environment • This situoid contains the substances `John` and `Mary` and a relational moment `kiss` which connects them. BUT: we have to add a certain environment and further activities. • Falling apple

  22. Situoids V Example 2 A part of the world capturing the life of tree in a certain environment. If a tree is considered as an organism, then the universals imply the viewpoint of a biologist and the granularity of branches, leaves, etc. (rather than electrons, atoms, etc.).

  23. Chronoids, Topoids • Chronoids are temporal durations • Topoids are spatial regions having a certain mereotopological structure AssumptionChronoids and topoids have no independent existence, they depend on the situoids which they frame

  24. Processes I • are constituents of situoidsA configuration C in the situoid S is defined as some result of taking a collection of substances and other individuals occurring in S and adding moments and material relations from S which serve to glue them together

  25. Processes II • are sequences of configurations Example 1: Football match Every football match is a sequence of configurations of 22 players and 1 ball within a suitable situoid and during a time interval of about 120 minutes (including the break)

  26. Processes III Example 2 An individual case of malaria is a concrete process realized by a sequence of configurations containing a person (a substance) within a situoid and certain changing moments associated with the disease.

  27. Material Relations • are individuals with the power of connecting entities Exampleskisses, contracts, conversations

  28. Refined Theory of Relations I • A relator is an individual connecting entities. A relator which has substances as arguments is of 1st order (these are exactly moments) A relator is of (n+1)st order if the heighest of the relators it relates es equal n AxiomAt least one of the arguments of a relator is an individual

  29. Refined Theory of Relations II • Let Rel be the class of all relators, and r,s be relators. r < s (s is stronger than r) iff r is among the arguments of s • Axiom:The ordering '< ' does not contain an infinite chain r1 < r2 < ...< rn <...

  30. Refined Theory of Relations III • Relations ( Formal relations, mediated relations) • Examples.

  31. Refined Theory of Relations IV • Examples

  32. Refined Theory of Relations V • Hierarchy of relations • Relations(formal, mediated) • Universals: Relator-Universals.

  33. Basic Relations I • x  y (membership relation) • x < y (part-of relation) • :< (x,y,z) (relativized part-of) • x :: y (instantiation) • :i (x,y) (inherence) • x y (framing) • x y (containment)

  34. Basic Relations II • x | y (framing) • x c y (containment) • :o (x,y) (location) • :h (x,y1, ..., yn) (holding) • :a (x,y) (association)

  35. Comparison to KIF • Basic Ontology of KIF • Most general category is a object • A set is a collection of objects • An individual is any object which is not a set • Functions and relations are finite sets of lists

  36. Comparison to Russell-Norvig

  37. Comparison to Sowas UO

  38. Comparison to LADSEB UO

  39. For more information about GOL please contact www.ontology.uni-leipzig.de Secretary: Birgit Binder Tel. +49 341 97 16104 Fax: +49 341 97 16130 E-mail: binder@IMISE.uni-leipzig.de Postal adress: Institute of Medical Informatics University of Leipzig Liebigstr. 27 04103 Leipzig, Germany

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