1. VT

2. http://ifomis.de Institute for Formal Ontology and Medical Information Science

3. IFOMIS Institute for Formal Ontology and Medical Information Science Faculty of Medicine University of Leipzig

4. 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)

5. Booleanism if F stands for a property and G stands for a property then F&G stands for a property FvG stands for a property not-F stands for a property F  G stands for a property and so on

6. Strong Booleanism There is a complete lattice of properties: self-identity FvG F G F&G non-self-identity

7. Strong Booleanism There is a complete lattice of properties: self-identity FvG not-F F G not-G F&G non-self-identity

8. Booleanism infects computer science, too Booleanism yields not ontology but F(a)ntology

9. Booleanism responsible, among other things, for Russell’s paradox Armstrong, D. Lewis free from Booleanism With their sparse theory of properties

10. 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

11. Standard semantics F stands for a property a stands for an individual properties belong to Platonic realm of forms or properties are sets of individuals for which F(a) is true (circularity)

12. 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

13. part Isa fly Used_for airplane Is_a_part_of bird Is_a_part_of building Is_a_part_of Ala (wing) SemU: 3232 Type: [Part] Part of an airplane SemU: 3268 Type: [Part] Part of a building SemU: D358 Type: [Body_part] Organ of birds for flying SemU: 3467 Type: [Role] Role in football player Isa Agentive Linguistic Ontologies SIMPLE make Agentive

14. part Isa fly Used_for airplane Is_a_part_of bird Is_a_part_of building Is_a_part_of Ala (wing) SemU: 3232 Type: [Part] Part of an airplane SemU: 3268 Type: [Part] Part of a building SemU: D358 Type: [Body_part] Organ of birds for flying SemU: 3467 Type: [Role] Role in football player Isa Agentive Linguistic Ontologies SIMPLE make Agentive

15. Reference Ontology An ontology is a theory of a domain of entities in the world Ontology is outside the computer seeks maximal expressiveness and adequacy to reality and sacrifices computational tractability for the sake of representational adequacy

16. Reference Ontology a theory of the tertium quid – called reality – needed to hand-callibrate database/terminology systems

17. Methodology Get ontology right first (realism; descriptive adequacy; rather powerful logic); solve tractability problems later

18. 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)

19. Domains of Current Work IFOMIS Leipzig: Medicine, Bioinformatics Laboratories for Applied Ontology Trento/Rome: Ontology of Cognition/Language Turin: Law Foundational Ontology Project: Space, Physics Ontology Works: Genetics, Molecular Biology Ontek Corporation: Biological Systematics Language and Computing: Natural Language Understanding

20. Two basic BFO oppositions Granularity (of molecules, genes, cells, organs, organisms...) SNAP vs. SPAN getting time right of crucial importance for medical informatics

22. 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

23. 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

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

25. Testing the BFO/MedO approach collaboration with Language and Computing nv (www.landcglobal.be)

26. 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.

27. L&C Technology FreePharma®, 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.

28. L&C statistical technology unearthed errors in SNOMED via pattern- recognition of semantic connections

29. 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

30. 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

31. 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

32. Three levels of ontology 1) 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.

33. L&C Medical Computational Linguistics Martin van Mol http://www.landcglobal.com

34. L&C’s long-term goal Transform the mass of unstructured patient records into a gigantic medical experiment

35. IFOMIS’s long-term goal Build a robust high-level BFO-MedO framework THE WORLD’S FIRST INDUSTRIAL- STRENGTH PHILOSOPHY which can serve as the basis for an ontologically coherent unification of medical knowledge and terminology

36. Research projects L&C Collaboration Standardization UMLS

37. 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.

38. 1. types of users 2. characteristics of users a. permanent (independent of experience with the software system) b. variable i. change independently of use of system (for example: age, disease state) ii. change with experience of use of system 3. types of user behavior a. behavior independent of the system b. behavior involving the system i. types of system use (keyboard actions, etc.) ii. other behavior involving the system (rejection, etc.) 4. contexts/environments of users a. contexts independent of the system b. contexts of system use

39. Functions from an Ontological Point of View Process-shapes Normal vs. Abnormal

40. The Theory of Granular Partitions Grids Mappings Closed World Assumption Knowledge-increase Complete and incomplete partitions

41. Mereotopological Theories for Medical Ontology Parts of anatomy of the human body Parts of physiology of the human body  Formal Theories for Layered Structures

42. The Ontology of the Gene Ontology Medical Ontology and Medical Anthropology Foundations of Spatiotemporal Ontology