vt. institute for formal ontology and medical information science

http://ifomis.de

Institute for Formal Ontology and Medical Information Science

IFOMIS

Institute for Formal Ontology and Medical Information ScienceFaculty of MedicineUniversity of Leipzig

First-order logic

F(a), G(a)R(a,b)

F(a) v G(a)F(a) & G(a)F(a) v xR(a,x)

Booleanism

if F stands for a property and G stands for a property

then F&G stands for a propertyFvG stands for a propertynot-F stands for a propertyFG stands for a propertyand so on

Strong Booleanism

There is a complete lattice of properties:

self-identity

FvG

F G

F&G

non-self-identity

Strong Booleanism

There is a complete lattice of properties:

self-identity

FvG

not-F F G not-G

F&G

non-self-identity

Booleanism infects computer science, too

Booleanism yields not ontologybut F(a)ntology

Booleanism

responsible, among other things, for Russell’s paradox

Armstrong, D. Lewis free from BooleanismWith their sparse theory of properties

Ontoquery

Affinities = restrictions on concept-combinations designed to avoid category

mistakes-- should avoid more

(e.g. recursive nonsense)p & (p v (p&p))

p p v p

Standard semantics

F stands for a propertya stands for an individual

properties belong to Platonic realm of formsorproperties are sets of individuals for which

F(a) is true (circularity)

How to solve the problem of Booleanism

Sharp distinction between genuine predicates (all of which are FORMAL, mainly relational predicates like '=')

and material predicates – which are eliminated via nominalization, and via quantification over universals

<parte>part

Isa

Isa

Isa

<volare>flyUsed_for

Used_for

<aeroplano>airplane

Is_a_part_of

<uccello>bird

Is_a_part_of

<edificio>building

Is_a_part_of

Ala (wing)

SemU: 3232Type: [Part]Part of an airplane

SemU: 3268Type: [Part]Part of a building

SemU: D358Type: [Body_part]Organ of birds for flying

SemU: 3467Type: [Role]Role in football

<giocatore>player

Isa

Agentive

Linguistic OntologiesSIMPLE

<fabbricare>make

Agentive

Reference Ontology

An ontology is a theory of a domain of entities in the worldOntology is outside the computerseeks maximal expressiveness and adequacy to realityand sacrifices computational tractability for the sake of representational adequacy

Reference Ontology

a theory of the tertium quid – called reality –

needed to hand-callibrate database/terminology systems

Methodology

Get ontology right first (realism; descriptive adequacy; rather

powerful logic);solve tractability problems later

The Reference Ontology Community

IFOMIS (Leipzig) Laboratories for Applied Ontology (Trento/Rome,

Turin)Foundational Ontology Project (Leeds)Ontology Works (Baltimore)Ontek Corporation (Buffalo/Leeds)Language and Computing (L&C)

(Belgium/Philadelphia)

Domains of Current Work

IFOMIS Leipzig: Medicine, BioinformaticsLaboratories for Applied Ontology

Trento/Rome: Ontology of Cognition/LanguageTurin: Law

Foundational Ontology Project: Space, PhysicsOntology Works: Genetics, Molecular BiologyOntek Corporation: Biological SystematicsLanguage and Computing: Natural Language

Understanding

Two basic BFO oppositions

Granularity (of molecules, genes, cells, organs, organisms ...)

SNAP vs. SPANgetting time right of crucial importance for medical informatics

BFO = SNAP/SPAN + Theory of Granular Partitions +

– theory of universals and instances – theory of part and whole– theory of boundaries– theory of functions, powers, qualities, roles– theory of environments– theory of spatial and spatiotemporal regions

MedO: medical domain ontology– universals and instances and normativity– theory of part and whole and absence– theory of boundaries/membranes– theory of functions, powers, qualities, roles,

(mal)functions, bodily systems– theory of environments: inside and outside the

organism– theory of spatial and spatiotemporal regions:

anatomical mereotopology

MedO: medical domain ontology– theory of granularity relations – between – molecule ontology– gene ontology– cell ontology– anatomical ontology– etc.

Testing the BFO/MedO approach

collaboration withLanguage and Computing nv

(www.landcglobal.be)

L&C’s ‘Semantic Indexing for Smart Information Retrieval and Extraction’ solution allows companies to more efficiently and accurately manage and retrieve documents. L&C also offers solutions for information analysis, document mining, information extraction, and coding.

L&C TechnologyFreePharma®, L&C’s natural language analyzer for

converting free text (spoken or typed) prescription and pharmacology information into XML.

FastCode®, L&C’s automated clinical coding product for translation of free text strings into ICD, SNOMED, MedDRA, etc.

LinKBase®, the largest formal medical knowledge base in the world, representing medicine in such a way that it is understandable for a computer.

LinKFactory®, L&C’s product suite for developing and managing large formal multilingual ontologies.

L&C statistical technology

unearthed errors in SNOMED via pattern-recognition of semantic connections

The Project

collaborate with L&C to show how an ontology constructed on the basis of philosophical principles can help in overhauling and validating the large terminology-based medical ontology LinkBase® used by L&C for NLP

L&C

LinKBase®: world’s largest terminology-based ontology with mappings to UMLS, SNOMED, etc.

+ LinKFactory®: suite for developing and managing large terminology-based ontologies

LinKBase

BFO and MedO designed to add better reasoning capacity

by tagging LinKBase domain-entities with corresponding BFO/MedO categories

by constraining links within LinKBase according to the theory of granular partitions

Three levels of ontology1) formal ontology, seeks the construction of a

framework of the categories – object, event, whole, part – employed in every domain,

2) domain ontology, a top-level system applying the structure of formal ontology to a particular domain, such as medicine or genetics,

3) terminology-based ontology, a very large, lower-level system dealing with the complete terminology of a given domain.

L&C Medical Computational Linguistics

Martin van Molhttp://www.landcglobal.com

L&C’s long-term goal

Transform the mass of unstructured patient records into a gigantic medical experiment

IFOMIS’s long-term goal

Build a robust high-level BFO-MedO framework

THE WORLD’S FIRST INDUSTRIAL-STRENGTH PHILOSOPHYwhich can serve as the basis for an ontologically coherent unification of medical knowledge and terminology

Research projects

L&C Collaboration

Standardization

UMLS

User Ontologies for Adaptive Interactive Software Systems

The problem: to extract information about users in a form that can be exploited by adaptive software.

Main current approach = the so-called stereotyping method has found most favour.

But its classifications are ad hoc and unprincipled, and they can be exploited by the adaptive system only after a large number of trials by various kinds of users.

The remedy is to create a database of user ontologies from which ready-made taxonomies can be constructed.

1. types of users2. characteristics of users

a. permanent (independent of experience with the software system)b. variablei. change independently of use of system(for example: age, disease state)ii. change with experience of use of system

3. types of user behaviora. behavior independent of the systemb. behavior involving the systemi. types of system use (keyboard actions, etc.)ii. other behavior involving the system (rejection, etc.)

4. contexts/environments of usersa. contexts independent of the systemb. contexts of system use

Functions from an Ontological Point of View

Process-shapesNormal vs. Abnormal

The Theory of Granular Partitions

GridsMappingsClosed World AssumptionKnowledge-increaseComplete and incomplete partitions

Mereotopological Theories for Medical Ontology

Parts of anatomy of the human bodyParts of physiology of the human body

Formal Theories for Layered Structures

The Ontology of the Gene Ontology Medical Ontology and Medical Anthropology

Foundations of Spatiotemporal Ontology

vt. institute for formal ontology and medical information science

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