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

Hierarchy of Universals

Universals

ColourSubstrate Space Time Shape . . .

solid gasfluid

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 III

• Relations ( Formal relations, mediated relations)

• Examples.

Refined Theory of Relations IV

• Examples

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

Comparison to Russell-Norvig

Comparison to Sowas UO

Comparison to LADSEB UO

For more information about GOL please contact

www.ontology.uni-leipzig.de

Secretary: Birgit BinderTel. +49 341 97 16104Fax: +49 341 97 16130E-mail: binder@IMISE.uni-leipzig.de

Postal adress: Institute of Medical InformaticsUniversity of LeipzigLiebigstr. 2704103 Leipzig, Germany