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VT
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
<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