Basic Formal Ontology Barry Smith http://ontologist.com March 2004

1. Basic Formal OntologyBarry Smithhttp://ontologist.comMarch 2004

3. The problem • Different communities of medical researchers use different and often incompatible category systems in expressing the results of their work

4. The solution • “ONTOLOGY” • Remove “Ontology Impedance” • But what does “ontology” mean?

5. Two alternative readings • Ontologies are oriented around terms or concepts = currently popular IT conception • Ontologies are oriented around the entities in reality = traditional philosophical conception, embraced also by IFOMIS

6. Ontology as a branch of philosophy • seeks to establish • the science of the kinds and structures of objects, properties, events, processes and relations in every domain of reality

7. Ontology a kind of generalized chemistry or zoology • (Aristotle’s ontology grew out of biological classification)

8. Aristotle world’s first ontologist

9. World‘s first ontology (from Porphyry’s Commentary on Aristotle’s Categories)

10. Linnaean Ontology

11. Ontology is distinguished from the special sciences it seeks to study all of the various types of entities existing at all levels of granularity

12. and to establish how they hang together to form a single whole (‘reality’ or ‘being’)

13. different concept/terminology systems

14. need not interconnect at all for example they may relate to entities of different granularity

15. we cannot make incompatible terminology-systems interconnect just by looking at concepts, or knowledge or language

16. we cannot make incompatible terminology-systems interconnect by staring at the terminology systems themselves

17. to decide which of a plurality of competing definitions to accept we need some tertium quid

18. we need, in other words, to take the world itself into account

19. BFO • = basic formal ontology

20. BFO • ontology is defined not as the ‘standardization’ or ‘specification’ of conceptualizations • (not as a branch of knowledge or concept engineering) • but as an inventory of the entities existing in reality

21. The BFO framework • will solve the problem of ontological impedance and provide tools for quality-control on the output of computer applications

22. BFO not a computer application • but a Reference Ontology • (something like old-fashioned metaphysics)

23. Reference Ontology • a theory of a domain of entities in the world

24. BFO • not just a system of categories • but a formal theory • with definitions, axioms, theorems • designed to provide the resources for reference ontologies for specific domains • of sufficient richness that terminological incompatibilities can be resolved intelligently rather than by brute force

25. Proposed solution • distinguish two separate tasks: • - the task of developing computer applications capable of running in real time • the task of developing an expressively rich framework of a sort which will allow us to resolve incompatibilities between definitions • and formulate intuitive and reliable principles for database curation

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

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

29. Realist Perspectivalism There is a multiplicity of ontological perspectives on reality, all equally veridical i.e. transparent to reality

30. Anatomy vs. Pathology

31. The Problem • The tumor developed in John’s lung over 25 years

32. The Problem • ____ developed in _____ over 25 years • process • state

33. The Problem • The tumor developed in the lung over 25 years • substances • things • objects • continuants

34. The Problem • The tumor developed in John’s lung over 25 years • PARTHOOD NOT DETERMINATE

35. processes The Problem • The tumor developed in the lung over 25 years • substances • GLUING THESE TOGETHER YIELDS ONTOLOGICAL MONSTERS

36. t i m e process Substances and processesexist in time in different ways substance

37. SNAP vs SPAN • Endurants vs perdurants • Continuants vs occurrents • In preparing an inventory of reality • we keep track of these two different kinds of entities in two different ways

38. No way in which sums of substances and processes can exist in time • … hence

39. Fourdimensionalism • – only processes exist • – time is just another dimension, analogous to the three spatial dimensions • – substances are analyzed away as worms/fibers within the four-dimensional plenum

40. There are no substances • Bill Clinton does not exist • Rather: there exists within the four-dimensional plenum a continuous succession of processes which are similar in a Billclintonizing way

41. Fourdimensionalism (the SPAN perspective) is right in everything it says • But incomplete

42. Realist Perspectivalism There is a multiplicity of ontological perspectives on reality, all equally veridical = transparent to reality

43. Need for different perspectives • Not one ontology, but a multiplicity of complementary ontologies • Cf. particle vs. wave ontologies in quantum mechanics

44. Two Orthogonal, Complementary Perspectives SNAP and SPAN

45. t i m e process Snapshot Video ontology ontology substance

46. SNAP and SPAN • stocks and flows • commodities and services • product and process • anatomy and physiology

47. SNAP and SPAN • SNAP entities • - have continuous existence in time • - preserve their identity through change • - exist in toto if they exist at all • SPAN entities • - have temporal parts • - unfold themselves phase by phase • - exist only in their phases/stages

48. You are a substance • Your life is a process • You are 3-dimensional • Your life is 4-dimensional

49. Many SNAP Ontologies t3 t2 t1 here time exists outside the ontology, as an index or time-stamp

50. includes everything which exists (present tense) each SNAPi section through reality