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VT 1 Ontology Barry Smith 2 Aristotle Aristotle author of The Categories 3 From Species to Genera animal bird canary 4 Species Genera as Tree animal bird canary fish ostrich 5 Species-genus trees can be represented also as map-like partitions 6 From Species to Genera animal bird canary 7 From Species to Genera animal bird canary 8 Species Genera as Tree animal bird canary fish ostrich 9 Species-Genera as Map/Partition animal bird fish canary ostrich 10 If Aristotelian realism is right, then such partitions are transparent to the reality beyond 11 Tree and Map/Partition 12 Alberti’s Grid c.1450 13 Coarse-grained Partition 14 Fine-Grained Partition 15 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) 16 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 17 Question: what other sorts of partitions have this feature of transparency? Answer: the partitions of common sense (folk biology, folk physics, folk psychology ...) 18 Aristotle Aristotle the ontologist of common-sense reality 19 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 20 The world of mothers, milk, and mice ... 21 The Empty Mask (Magritte) milk mama mouse Mount Washington 22 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 23 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 24 Natural categories have borderline cases sparrow ostrich birds 25 ... they have a kernel/penumbra structure penumbra of borderline cases kernel of focal instances 26 every cell in every common-sense partition is subject to this same kernel-penumbra structure: animal bird fish canary ostrich 27 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 28 but more: 29 in addition to objects (substances), which pertain to what a thing is at all times at which it exists: cow man rock planet 30 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 31 An accident = what holds of a substance per accidens 32 Nine Accidental Categories quid? quantum? quale? ad quid? ubi? quando? in quo situ? in quo habitu? quid agit? quid patitur? substance quantity quality relation place time status/context habitus action passion 33 Substances are the bearers of accidents hunger John = relations of inherence (one-sided existential dependence) 34 Both substances and accidents instantiate universals at higher and lower levels of generality 35 species, genera substance organism animal mammal cat siamese frog instances 36 common nouns Common nouns substance organism animal mammal cat pekinese proper names 37 types substance organism animal mammal cat siamese frog tokens 38 Our clarification accidents to be divided into two large and essential distinct families of QUALITIES and PROCESSES 39 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) 40 Substance universals pertain to what a thing is at all times at which it exists: cow man rock planet VW Golf 41 Quality universals pertain to how a thing is at some time at which it exists: red hot suntanned spinning Clintophobic Eurosceptic 42 Process universals reflect invariants in the spatiotemporal world taken as an atemporal whole football match course of disease exercise of function (course of) therapy 43 Processes and qualities, too, instantiate genera and species Thus process and quality universals form trees 44 Accidents: Species and instances quality color red scarlet R232, G54, B24 this individual accident of redness (this token redness – here, now) 45 substance accidents one substantial category John, man nine accidental categories hunger, your hunger, being hungry your sun-tan your being taller than Mary 46 substance John accidents quantity (two feet long) quality (white) time (yesterday) position (is sitting) relation (taller than) place (in the Lyceum) possession (has shoes on) action (cuts) passion (is cut) 47 substance Bearers accidents Substances are the bearers of accidents 48 substance Bearers accidents Substances are the bearers of accidents hunger John = relations of inherence (one-sided existential dependence) 49 substance s 50 Substance + Accident = State of Affairs States of Affair setting into relief s 51 Prototypicality among instances too albino frog instances 52 Aristotle 1.0 an ontology recognizing: substance tokens accident tokens substance types accident types 53 Is everything in commonsense reality either a substance or an accident? 54 well, what about artefacts ? 55 Standard Aristotelian theory of artefacts: artefacts are mereological sums of substances 56 Positive and negative parts positive part (made of matter) negative part or hole (not made of matter) 57 Nine Accidental Categories quid? quantum? quale? ad quid? ubi? quando? in quo situ? in quo habitu? quid agit? quid patitur? substance quantity quality relation place time status/context habitus action passion 58 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) 59 What is missing from Aristotle? Gibson: affordances niches Barker: behavior settings 60 Places are holes 61 niches, environments are holes 62 The metaphysics of holes 63 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 64 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) 65 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 reference vs. theory 66 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 67 Both scientific partitions and common-sense partitions are based on reference-systems which have survived rigorous empirical tests 68 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? 69 Aristotle 2000 70 animal Universe/Periodic Table bird fish folk biology canary ostrich partition of DNA space 71 animal Universe/Periodic Table bird fish canary ostrich both are transparent partitions of one and the same reality 72 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 73 relative hylomorphism substances and accidents reappear in the microscopic and macroscopic worlds of e.g. molecular biology and astronomy (Aristotelian ontological zooming) 74 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 75 Perspectivalism Perspectivalism Different partitions may represent cuts through the same reality which are skew to each other 76 An organism is a totality of atoms 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 77 all express partitions which are transparent, at different levels of granularity, to the same reality beyond 78 Coarse-grained Partition what happens when a fringe instance arises ? 79 Coarse-grained Partition what happens when a fringe instance arises ? Aristotle 1.0: you shrug your shoulders 80 Aristotle 2000: you go out to find a finer grained partition which will recognize the phenomenon in question as prototypical 81 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 82 IFOMIS Institute for Formal Ontology and Medical Information Science Faculty of Medicine University of Leipzig http://ifomis.de 83 The Idea Computational medical research will transform the discipline of medicine … but only if communication problems can be solved 84 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 85 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) 86 First ontology (from Porphyry’s Commentary on Aristotle’s Categories) 87 Linnaean Ontology 88 Medical Diagnostic Ontology 89 Example: The Gene Ontology (GO) hormone ; GO:0005179 %digestive hormone ; GO:0046659 %peptide hormone ; GO:0005180 %adrenocorticotropin ; GO:0017043 %glycopeptide hormone ; GO:0005181 %follicle-stimulating hormone ; GO:0016913 90 as tree hormone digestive hormone adrenocorticotropin peptide hormone glycopeptide hormone follicle-stimulating hormone 91 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 92 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 93 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 94 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 95 Methodology Get ontology right first (realism; descriptive adequacy; rather powerful logic); solve tractability problems later 96 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) 97 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 98 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 99 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 100 MedO including sub-ontologies: cell ontology drug ontology protein ontology gene ontology 101 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 stampcollecting) 102 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 103