1 VT

2 Ontology Barry Smith

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

4 The Idea Computational medical research will transform the discipline of medicine … but only if communication problems can be solved

5 Medicine desperately needs to find a way to enable the huge amounts of data resulting from trials by different groups to be (f)used together

6 How resolve incompatibilities? Whole Industry of ‘Ontologies’ in contemporary information science “ONTOLOGY” = the solution of first resort (compare: kicking a television set) But what does ‘ontology’ mean? Current most popular answer: a hierarchy of concepts (a thesaurus, a list of terms)

7 Aristotle author of The Categories Aristotle

8 From Species to Genera canary animal bird

9 Species Genera as Tree canary animal bird fish ostrich

10 genus Species-genus trees can be represented also as map-like partitions

11 From Species to Genera canary animal bird

12 From Species to Genera animal bird canary

13 Species Genera as Tree canary animal bird fish ostrich

14 Species-Genera as Map/Partition animal bird canary ostrich fish canary

15 If Aristotelian realism is right, then such partitions are transparent to the reality beyond

16 Tree and Map/Partition

17 Alberti’s Grid c.1450

18 Coarse-grained Partition

19 Fine-Grained Partition

20 Scientific theories comprehend in their underlying category systems veridical partitions of reality often there are many veridical partitions of reality, cross-cutting each other, differing only in nuances)

21 What is a gene? GDB: a gene is a DNA fragment that can be transcribed and translated into a protein Genbank: a gene is a DNA region of biological interest with a name and that carries a genetic trait or phenotype (from Schulze-Kremer) GO does not tell us which of these is correct, or indeed whether either is correct, and it does not tell us how to integrate data from the corresponding sources

22 Question: what other sorts of partitions have this feature of transparency? the partitions of common sense (folk biology, folk physics, folk psychology...) Answer:

23 Aristotle the ontologist of common-sense reality Aristotle

24 The world we grasp in natural language = the world as apprehended via that conceptualization we call common sense = the normal environment (the niche) shared by children and adults in everyday perceiving and acting

25 The world of mothers, milk, and mice...

26 The Empty Mask (Magritte) mama mouse milk Mount Washington

27 our common-sense partition of the world of common sense is transparent (common sense, like science, is [mostly*] true) mothers exist... * “mostly” because of the problem of vagueness

28 Problem of vagueness solved by recognizing that our categories apply to reality in such a way as to respect an opposition... between standard or focal or prototypical instances... and non-standard or ‘fringe’ instances

29 birds ostrich Natural categories have borderline cases sparrow

30... they have a kernel/penumbra structure kernel of focal instances penumbra of borderline cases

31 animal bird canary ostrich fish every cell in every common-sense partition is subject to this same kernel-penumbra structure:

32 What is common-sense reality? the mesoscopic space of everyday human action and perception – a space centered on objects organized into hierarchies of species and genera... and subject to prototypicality

33 but more:

34 in addition to objects (substances), which pertain to what a thing is at all times at which it exists: cow man rock planet

35 the common-sense world contains also accidents which pertain to how a thing is at some time at which it exists: red hot suntanned spinning

36 An accident = what holds of a substance per accidens

37 quid? substance quantum? quantity quale? quality ad quid? relation ubi? place quando? time in quo situ? status/context in quo habitu? habitus quid agit? action quid patitur? passion Nine Accidental Categories

38 = relations of inherence (one-sided existential dependence) John hunger Substances are the bearers of accidents

39 Both substances and accidents instantiate universals at higher and lower levels of generality

40 siamese mammal cat organism substance species, genera animal instances frog

41 Common nouns pekinese mammal cat organism substance animal common nouns proper names

42 siamese mammal cat organism substance types animal tokens frog

43 Our clarification accidents to be divided into two large and essential distinct families of QUALITIES and PROCESSES

44 There are universals both among substances (man, mammal) and among qualities (hot, red) and among processes (run, movement) There are universals also among spatial regions (triangle, room, cockpit) and among spatio-temporal regions (orbit)

45 Substance universals pertain to what a thing is at all times at which it exists: cow man rock planet VW Golf

46 Quality universals pertain to how a thing is at some time at which it exists: red hot suntanned spinning Clintophobic Eurosceptic

47 Process universals reflect invariants in the spatiotemporal world taken as an atemporal whole football match course of disease exercise of function (course of) therapy

48 Processes and qualities, too, instantiate genera and species Thus process and quality universals form trees

49 Accidents: Species and instances quality color red scarlet R232, G54, B24 this individual accident of redness (this token redness – here, now)

50 substance one substantial category John, man nine accidental categories hunger, your hunger, being hungry your sun-tan your being taller than Mary accidents

51 substance place (in the Lyceum) time (yesterday) position (is sitting) possession (has shoes on) action (cuts) passion (is cut) quantity (two feet long) quality (white) relation (taller than) John accidents

52 substance Substances are the bearers of accidents accidents Bearers

53 substance Substances are the bearers of accidents accidents John = relations of inherence (one-sided existential dependence) Bearers hunger

54 s substance

55 Substance + Accident = State of Affairs setting into relief States of Affair s

56 instances Prototypicality among instances too albino frog

57 Aristotle 1.0 an ontology recognizing: substance tokens accident tokens substance types accident types

58 Is everything in common- sense reality either a substance or an accident?

59 well, what about artefacts ?

60 Standard Aristotelian theory of artefacts: artefacts are mereological sums of substances

61 Positive and negative parts positive part negative part or hole (made of matter) (not made of matter)

62 quid? substance quantum? quantity quale? quality ad quid? relation ubi? place quando? time in quo situ? status/context in quo habitu? habitus quid agit? action quid patitur? passion Nine Accidental Categories

63 Places For Aristotle the place of a substance is the interior boundary of the surrounding body (for example the interior boundary of the surrounding water where it meets a fish’s skin)

64 What is missing from Aristotle? Gibson: affordances niches Barker:behavior settings

65 Places are holes

66 niches, environments are holes

67 The metaphysics of holes

68 Aristotle 1.5 an ontology of substances + accidents + holes (and other entities not made of matter) + fiat and bona fide boundaries + artefacts and environments is true

69 folk biology Aristotelian folk biology, folk physics, folk psychology, etc., are true of the common-sense world as it currently exists (they have nothing to offer regarding its pre-history, its long term evolution, its position in the cosmos)

70 reference vs. theory They have not much to offer, either, by way of good explanatory theories of the entities in their respective domains, but they are transparent to those domains nonetheless

71 reference realism vs. theory realism this distinction applied not only to science (against T. S. Kuhn et al.) but also to common sense (against sceptics of various stripes) the sun exists, and has existed for a long time – the very same object

72 Both scientific partitions and common-sense partitions are based on reference-systems which have survived rigorous empirical tests

73 The $64000 Question How do those parts and dimensions of reality which we call the common-sense world... relate to those parts and dimensions of reality which are studied by science?

74 Aristotle 2000

75 Universe/Periodic Table animal bird canary ostrich fish folk biology partition of DNA space

76 Universe/Periodic Table animal bird canary ostrich fish both are transparent partitions of one and the same reality

77 many transparent partitions at different levels of granularity will operate with species-genus hierarchies and with an ontology of substances (objects) and accidents (attributes, processes) along the lines described by Aristotle

78 relative hylomorphism substances and accidents reappear in the microscopic and macroscopic worlds of e.g. molecular biology and astronomy (Aristotelian ontological zooming)

79 we do not assert that every level of granularity is structured in substance-accident form -- perhaps there are pure process levels, perhaps there are levels structured as fields

80 Perspectivalism Different partitions may represent cuts through the same reality which are skew to each other

81 An organism is a totality of molecules An organism is a totality of cells An organism is a single unitary substance... all of these express veridical partitions An organism is a totality of atoms

82 all express partitions which are transparent, at different levels of granularity, to the same reality beyond

83 Coarse-grained Partition what happens when a fringe instance arises ?

84 Coarse-grained Partition what happens when a fringe instance arises ? Aristotle 1.0: you shrug your shoulders

85 Aristotle 2000: you go out to find a finer grained partition which will recognize the phenomenon in question as prototypical

86 The advance of science is not an advance away from Aristotle towards something better. Provided Aristotle is interpreted aright, it is a rigorous demonstration of the correctness of his ontological approach

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

88 The Idea Computational medical research will transform the discipline of medicine … but only if communication problems can be solved

89 Medicine desperately needs to find a way to enable the huge amounts of data resulting from trials by different groups to be (f)used together

90 How resolve incompatibilities? Ganze Industrie von ‘Ontologien’ in der heutigen Informationswissenschaft “ONTOLOGY” = the solution of first resort (compare: kicking a television set) But what does ‘ontology’ mean? Current most popular answer: a hierarchy of concepts (a thesaurus, a list of terms)

91 First ontology ( from Porphyry’s Commentary on Aristotle’s Categories)

92 Linnaean Ontology

93 Medical Diagnostic Ontology

94 Example: The Gene Ontology (GO) hormone ; GO: %digestive hormone ; GO: %peptide hormone ; GO: %adrenocorticotropin ; GO: %glycopeptide hormone ; GO: %follicle-stimulating hormone ; GO:

95 as tree hormone digestive hormone peptide hormone adrenocorticotropin glycopeptide hormone follicle-stimulating hormone

96 Gene Ontology Cellular Component Ontology: subcellular structures, locations, and macromolecular complexes; examples: nucleus, telomere Molecular Function Ontology: tasks performed by individual gene products; examples: transcription factor, DNA helicase Biological Process Ontology: broad biological goals accomplished by ordered assemblies of molecular functions; examples: mitosis, purine metabolism

97 Problem: There exist multiple databases genomic cellular structural phenotypic … and even for each specific type of information, e.g. DNA sequence data, there exist several databases of different scope and organisation

98 What is a gene? GDB: a gene is a DNA fragment that can be transcribed and translated into a protein Genbank: a gene is a DNA region of biological interest with a name and that carries a genetic trait or phenotype GO does not tell us which of these is correct, or indeed whether either is correct, and it does not tell us how to integrate data from the corresponding sources

99 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

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

101 The Reference Ontology Community IFOMIS (Leipzig) Laboratories for Applied Ontology (Trento/Rome, Turin) Foundational Ontology Project (Leeds) Ontology Works (Baltimore) BORO Program (London) Ontek Corporation (Buffalo/Leeds) LandC (Belgium/Philadelphia)

102 Recall: GDB: a gene is a DNA fragment that can be transcribed and translated into a protein Genbank: a gene is a DNA region of biological interest with a name and that carries a genetic trait or phenotype

103 Ontology Note that terms like ‘fragment’, ‘region’, ‘name’, ‘carry’, ‘trait’, ‘type’ … along with terms like ‘part’, ‘whole’, ‘function’, ‘substance’, ‘inhere’ … are ontological terms in the sense of traditional (philosophical) ontology

104 Three types of reference ontology 1. formal ontology = framework for definition of the highly general concepts – such as object, event, part – employed in every domain 2. domain ontology, a top-level theory with a few highly general concepts from a particular domain, such as genetics or medicine 3. terminology-based ontology, a very large theory embracing many concepts and inter-concept relations

105 MedO including sub-ontologies: cell ontology drug ontology protein ontology gene ontology

106 and sub-ontologies: anatomical ontology epidemiological ontology disease ontology therapy ontology pathology ontology the whole designed to give structure to the medical domain (currently medical education comparable to stamp- collecting)

107 If sub-domains like these cell ontology drug ontology protein ontology gene ontology are to be knitted together within a single theory, then we need also a theory of granularity