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From Formal Ontology to Biomedical Ontology

From Formal Ontology to Biomedical Ontology. Biomereology. Barry Smith http://ifomis.org. Mereology as Formal Ontology. Logical Investigations (1900-01) Investigation III: On the Theory of Wholes and Parts. Husserl. Le śniewski Kotarbiński Tarski Grzegorczyk Woodger.

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From Formal Ontology to Biomedical Ontology

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  1. From Formal Ontology to Biomedical Ontology Biomereology Barry Smith http://ifomis.org

  2. Mereology as Formal Ontology • Logical Investigations (1900-01) • Investigation III: • On the Theory of Wholes and Parts

  3. Husserl • Leśniewski • Kotarbiński • Tarski • Grzegorczyk • Woodger

  4. Cantor Leśniewski • Frege early Tarski • late Carnap (geometry of solids) • Grzegorczyk • (mereotopology) • set-theory as mereology as • principal instrument principal instrument • of formal ontology of formal ontology

  5. Hilbert Leśniewski • late Tarski Russell • Carnap early Tarski • Putnam Woodger • contemporary contemporary • model-theoretic realist ontology • semantics

  6. For Frege, Russell, Leśniewski, Wittgenstein, Quine … • logic is a zoology of facts • formal theories are theories of reality • with one intended interpretation: the world tragically after starting off on the right road

  7. Logic took a wrong turn

  8. (Tarski) • Carnap, Putnam, Goodman, etc.: • Forget reality! • Lose yourself in ‘models’! • “internal realism” ...

  9. Hilbert Leśniewski • late Tarski Russell • Carnap Wittgenstein • Putnam Quine • OLD: Logic as • Language

  10. Hilbert Leśniewski • late Tarski Russell • Carnap Wittgenstein • Putnam Quine • NEW: Logic as • Calculus

  11. Hilbert Leśniewski • late Tarski Russell • Carnap Wittgenstein • Putnam Quine • OLD: Set-theory- • based-model- • theoretic semantics • ... possible worlds • blah blah

  12. Hilbert Leśniewski • late Tarski Russell • Carnap early Tarski • Putnam Woodger • NEW: Extreme • Mereotopological • Bio-Ontological Realism

  13. Husserl + Leśniewski • realist mereology-based ontology • + universals • + topology • + relations • + dependent entities

  14. Formal Ontology vs. Formal Logic • Formal ontology deals with formal ontological structures • Formal logic deals with formal logical structures • ‘formal’ = domain-neutral • (obtain in all material spheres of reality)

  15. Formal Ontology • the theory of those ontological structures • (such as part-whole, universal-particular) • which apply to all domains whatsoever

  16. Formal Ontology vs. Formal Logic • Formal ontology deals with the interconnections of things • with objects and properties, parts and wholes, relations and collectives

  17. Formal-Ontological Categories • object • state of affairs • unity • plurality • boundary • dependent part • independent part • relation • are able to form complex structures in non-arbitrary, law-governed ways

  18. From Formal Ontology • to Biomedical Ontology

  19. Organism Organ Tissue 10-1 m Cell Organelle 10-5 m Protein DNA 10-9 m Scales of anatomy

  20. Complexity of biological structures • 30,000 genes in human • 200,000 proteins • 100s of cell types • 100,000s of disease types • 1,000,000s of biochemical pathways (including disease pathways) A new golden age of classification

  21. A new golden age of classification central importance of classes / types / kinds / universals / species of independent objects dependent objects processes

  22. Different scientificcultures / terminologies • immunology genetics cell biology

  23. Fleck on Thought-Styles • the general structure of a thought-collective entails that the communication of thoughts within the collective, irrespective of content or logical justification, leads for sociological reasons to the reinforcement of the thought structure

  24. The problem of the unity of science • The logical positivist solution to this problem addressed a world in which sciences are identified with • printed texts • What if sciences are identified with • information systems ?

  25. Problem • Each (clinical, pathological, genetic, proteomic, pharmacological …) information system uses its own classification system • How can we overcome the incompatibilities which become apparent when data from distinct sources needs to be combined?

  26. Solution: • “Ontology”

  27. Compare: • pure mathematics (theories of structures such as order, set, function, mapping) employed in every domain • applied mathematics, applications of these theories = re-using the same definitions, theorems, proofs in new application domains

  28. Three levels of ontology • formal ontology (mereology, mereotopology, …) • 2)domain ontologies • = Foundational Model of Anatomy, Gene Ontology, Unified Medical Language System, SNOMED

  29. Biomereology must be rich enough to deal with time and change

  30. Leśniewski’s mereology • grew out of his concerns with the foundations of mathematics • LIKE SET THEORY, IT DOES NOT TAKE ACCOUNT OF TIME

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

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

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

  34. The Problem • The tumor developed in the lung over 25 years • WHAT IS PART OF WHAT • IS NOT DETERMINATE

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

  39. 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 sort of way

  40. Fourdimensionalism solves the problems of universal applicability of mereologyindeterminacy of parthood

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

  42. The response to anyone who believes that fourdimensionalism is the whole truth about reality is: • see a doctor

  43. The response to anyone who believes that fourdimensionalism is the whole truth about reality is: • see any organism

  44. Bio-Ontology requires two orthogonal applications of mereologyA fourdimensional ontologysupplemented by a threedimensional ontology of continuant entities

  45. How can a threedimensional ontology solve the problem of determinacy of parthood • PARTHOOD AT AN INSTANT IS DETERMINATE • take an assay of what exists in the three spatial dimensions always at some specific instant of time

  46. The 4D and 3D ontologies represent two complementary views • of the same rich and messy reality

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