1 From Formal Ontology to Biomedical Ontology Barry Smith Biomereology

2

3 Mereology as Formal Ontology Logical Investigations ( ) Investigation III: On the Theory of Wholes and Parts

4 Husserl Leśniewski Kotarbiński Tarski Grzegorczyk Woodger

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

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

7 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

8

9 Logic took a wrong turn

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

11 Hilbert Leśniewski late Tarski Russell Carnap Wittgenstein Putnam Quine OLD: Logic as Language

12 Hilbert Leśniewski late Tarski Russell Carnap Wittgenstein Putnam Quine NEW: Logic as Calculus

13

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

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

16

17 Husserl + Leśniewski realist mereology-based ontology + universals + topology + relations + dependent entities

18 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)

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

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

21 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

22 From Formal Ontology to Biomedical Ontology

23 Scales of anatomy DNA Protein Organelle Cell Tissue Organ Organism m m m

24 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

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

26 Different scientific cultures / terminologies immunology genetics cell biology

27 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

28 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 ?

29 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?

30 Solution: “Ontology”

31 Compare: 1)pure mathematics (theories of structures such as order, set, function, mapping) employed in every domain 2)applied mathematics, applications of these theories = re-using the same definitions, theorems, proofs in new application domains

32 Three levels of ontology 1)formal ontology (mereology, mereotopology, …) 2) domain ontologies = Foundational Model of Anatomy, Gene Ontology, Unified Medical Language System, SNOMED

33 Biomereology must be rich enough to deal with time and change

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

35 The Problem The tumor developed in John’s lung over 25 years

36 The Problem ____ developed in _____ over 25 years process

37 The Problem The tumor developed in the lung over 25 years substances things objects continuants

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

39 The Problem The tumor developed in the lung over 25 years substances GLUING THESE TOGETHER MEREOLOGICALLY YIELDS ONTOLOGICAL MONSTERS processes

40 Substances and processes exist in time in different ways substance t i m e process

41 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

42 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

43 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

44 Fourdimensionalism solves the problems of universal applicability of mereology indeterminacy of parthood

45 Fourdimensionalism (the SPAN perspective) is right in everything it says But incomplete

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

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

48 Bio-Ontology requires two orthogonal applications of mereology A fourdimensional ontology supplemented by a threedimensional ontology of continuant entities

49 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

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

51 DNA Protein Organelle Cell Tissue Organ Organism m m Scales of anatomy m

52 A new golden age of classification central importance of classes / types / kinds / universals / species

53 and of is-a hierarchies

54

55

56 cars Cadillacs blue cars blue Cadillacs

57 Confusions about ‘is-a’ and ‘part-of’ in bio-ontologies Unified Medical Language System

58 The UMLS Semantic Network a US Federal Government ontology designed to unify all biomedical terminologies

59 what are the nodes in this graph?

60

61 linguistic entities ≈ meanings

62 UMLS SN is_a = def. if one item ‘is_a’ another item then the first item is more specific in meaning than the second item

63 Fruit Orange Vegetable SimilarTo Apfelsine SynonymWith NarrowerThan Goble & Shadbolt

64

65 How can concepts/meanings figure as relata of relations such as disrupts or contained in?

66 Swimming is healthy and contains 8 letters

67 UMLS Semantic Network

68 Vitamin Injury or Poisoning causes

69 Bacterium Experimental Model of Disease causes

70 Manufactured Object Disease or Syndrome causes

71 Biomedical or Dental Material Mental or Behavioral Dysfunction causes

72 The Gene Ontology a ‘controlled vocabulary’ designed to standardize annotation of genes and gene products used by over 20 genome database and many other groups in academia and industry and methodology much imitated

73 A part_of B =def A can be part of B

74 The Gene Ontology menopause part_of death

75 GO: ‘within’ lytic vacuole within a protein storage vacuole is-a protein storage vacuole interval within a football match is-a football match embryo within a uterus is-a uterus

76 GO: ‘extrinsic to’ extrinsic to membrane part-of membrane

77 these people need our help formal-ontological help

78 Woodger The Axiomatic Method in Biology part_of earlier_than derives_by_division_or _fusion_from environment_of is_a_cell is_a_male_gamete is_a_female_gamete is_a_whole_organism is_an_organized_unity is_a_genetic_property

79 Material Primitives part_of earlier_than derives_by_division_or _fusion_from environment_of is_a_cell is_a_male_gamete is_a_female_gamete is_a_whole_organism is_an_organized_unity is_a_genetic_property

80 Formal Primitives part_of earlier_than derives_by_division_or _fusion_from environment_of is_a_cell is_a_male_gamete is_a_female_gamete is_a_whole_organism is_an_organized_unity is_a_genetic_property

81 Formal Primitives part_of earlier_than derives_by_division_or _fusion_from environment_of is_a_cell is_a_male_gamete is_a_female_gamete is_a_whole_organism is_an_organized_unity is_a_genetic_property

82 Open Biological Ontologies Consortium OBO library of controlled vocabularies developed for shared use across different biological domains. Gene Ontology plus: Cell Ontology, Sequence Ontology, etc.

83 Open Biological Ontologies Consortium European Bioinformatics Institute, Cambridge Jackson Labs, Bar Harbor, Maine Berkeley Genetics, Edinburgh Mouse Atlas Project IFOMIS, Saarbrücken

84 OBO Relations Ontology: is_a part_of develops_ from derives_ from located_at participates_in adjacent_to contained_in precedes has_function

85 Woodger’s Formal Primitives part_of earlier_than derives_by_division_or _fusion_from environment_of is_a_cell is_a_male_gamete is_a_female_gamete is_a_whole_organism is_an_organized_unity is_a_genetic_property

86 Foundational Model of Anatomy Reference Ontology a graph-theoretical structure involving two sorts of links or edges: is-a (= is a subtype of ) (auditory ossicle is-a bone) part-of (cervical vertebra part-of vertebral column)

87 Pleural Cavity Pleural Cavity Interlobar recess Interlobar recess Mesothelium of Pleura Mesothelium of Pleura Pleura(Wall of Sac) Pleura(Wall of Sac) Visceral Pleura Visceral Pleura Pleural Sac Parietal Pleura Parietal Pleura Anatomical Space Organ Cavity Organ Cavity Serous Sac Cavity Serous Sac Cavity Anatomical Structure Anatomical Structure Organ Serous Sac Mediastinal Pleura Mediastinal Pleura Tissue Organ Part Organ Subdivision Organ Subdivision Organ Component Organ Component Organ Cavity Subdivision Organ Cavity Subdivision Serous Sac Cavity Subdivision Serous Sac Cavity Subdivision

88 Pleural Cavity Pleural Cavity Interlobar recess Interlobar recess Mesothelium of Pleura Mesothelium of Pleura Pleura(Wall of Sac) Pleura(Wall of Sac) Visceral Pleura Visceral Pleura Pleural Sac Parietal Pleura Parietal Pleura Anatomical Space Organ Cavity Organ Cavity Serous Sac Cavity Serous Sac Cavity Anatomical Structure Anatomical Structure Organ Serous Sac Mediastinal Pleura Mediastinal Pleura Tissue Organ Part Organ Subdivision Organ Subdivision Organ Component Organ Component Organ Cavity Subdivision Organ Cavity Subdivision Serous Sac Cavity Subdivision Serous Sac Cavity Subdivision

89 Pleural Cavity Pleural Cavity Interlobar recess Interlobar recess Mesothelium of Pleura Mesothelium of Pleura Pleura(Wall of Sac) Pleura(Wall of Sac) Visceral Pleura Visceral Pleura Pleural Sac Parietal Pleura Parietal Pleura Anatomical Space Organ Cavity Organ Cavity Serous Sac Cavity Serous Sac Cavity Anatomical Structure Anatomical Structure Organ Serous Sac Mediastinal Pleura Mediastinal Pleura Tissue Organ Part Organ Subdivision Organ Subdivision Organ Component Organ Component Organ Cavity Subdivision Organ Cavity Subdivision Serous Sac Cavity Subdivision Serous Sac Cavity Subdivision

90 The Anatomy Reference Ontology a coherent theory of part-of as a relation between classes / types must be based on a (mereological) theory of part-of as a relation between instances Mary’s heart part-of Mary

91 Taking the instance-level part_of as primitive we can define: A part_of B = any instance of A is part_of some instance of B nucleus part_of cell but not: testis part_of human

92 from A part_of B we cannot infer that B has_part A human_testis part_of human but not human has_part human testis running has_part breathing but not breathing part_of running

93 Scales of anatomy DNA Protein Organelle Cell Tissue Organ Organism m m m

94 Institute for Formal Ontology and Medical Information Science

95 Buffalo Center for Ontological Research Two tenure-track faculty positions in ontology

96 The End