gol a general ontological language barry smith department of philosophy university of buffalo...
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GOLA General Ontological Language
Barry Smith
Department of Philosophy
University of Buffalo
Heinrich Herre
Inst. of Medical Informatics
University of Leipzig
Barbara Heller
Inst. of Medical Informatics
University of Leipzig
Wolfgang Degen
Inst. of Theoretical Informatics
University of Erlangen
Contents
• Aims and Motivation
• Application Scenario
• Sets, Individuals, Universals
• Basic Types of Individuals
• Basic Types of Relations
• Comparison to Upper-Level Ontologies
• Future Research
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
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
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
Information and Communication Services based on Data Dictionaries
Data InputRequests
Acknowledgement
Participants
Clinics, Oncol. SpecialistsPrimary PathologistsRadio TherapistsSelf-help GroupsPatients & Relatives
I N T E R N E T
Information Services
NotificationDocumentation
Data Dictionaries
Communication ServicesData Bases
DepositionsDocuments
Participants‘SpecificQuery
Judgement Notification
Reference Centres
Reference-RX
Reference-Pathology
Reference-Laboratories
Heterogenous Data Bases
Clinical Trial Centres
Morbus Hodgkin
Hm-NHL
Lm-NHLHeterogenous Data Bases
Patient DataPatient Data
Material
Electonical dispatch
Material dispatch (conventional)
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
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
Ontology versus Set Theory
The facile translation of ontological relations into sets removes the possibility of our gaining insight into reality
Hierarchy of Categories
Top-Category
RelationEntity
Set Urelement
Universal Individual
TopoidSubstance Moment Chronoid Situoid
formal material
Sets and Urelements I
Sets• abstract entitiesabstract entities• independent of space and timeindependent of space and time• determined by their extensionsdetermined by their extensions
UrelementsUrelements• not setsnot sets• have internal structure which the have internal structure which the
membership relation cannot unfoldmembership relation cannot unfold
Sets and Urelements II
Basic Axiom
For every finite collection of entities there exists a set containing them as elements
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
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}
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
Moments
• can exist only in a substance
• are dynamic
• can be lost over time
Examplesactions, passions, a blush, a handshake, a thought
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
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
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)
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
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.).
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
Processes I
• are constituents of situoids
A 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
Processes II
• are sequences of configurations
Example 1: Football matchEvery 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)
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.
Material Relations
• are individuals with the power of connecting entities
Exampleskisses, contracts, conversations
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
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 <...
Refined Theory of Relations V
• Hierarchy of relations
• Relations(formal, mediated)
• Universals: Relator-Universals.
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)
Basic Relations II
• x | y (framing)
• x c y (containment)
• :o (x,y) (location)
• :h (x,y1, ..., yn) (holding)
• :a (x,y) (association)
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
For more information about GOL please contact
www.ontology.uni-leipzig.de
Secretary: Birgit BinderTel. +49 341 97 16104Fax: +49 341 97 16130E-mail: [email protected]
Postal adress: Institute of Medical InformaticsUniversity of LeipzigLiebigstr. 2704103 Leipzig, Germany