Ontology as a Branch of Philosophy


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Forms part of a training course in ontology given in Buffalo in 2009. For details and accompanying video see http://ontology.buffalo.edu/smith/IntroOntology_Course.html

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  • Porphyry‘s Tree Ca. 1514
  • http://www.kheper.auz.com/gaia/biosphere/systematics/Linnean.htm
  • From: http://www.cinemedia.net/SFCV-RMIT-Annex/rnaughton/DRAWING_MACHINES.htm from P. Le Dubreuil, La Perspective Pratique (Paris 1642)
  • http://www.proformacorp.com/whtpap1.htm Enterprise Application Modeling
  • Inner Gorge, Colorado River, Granite Rapids, looking west from Tonto Trail just west of Salt Creek http//www.kaibab.org/gc/images/img0072.jpg
  • Florence
  • http://rprcsgi.rprc.washington.edu/~atlas
  • http://www.corrosionsource.com/handbook/periodic/periodic_table.gif
  • http://www2.iicm.edu/ivis/ivis/node25.htm
  • http://www2.iicm.edu/ivis/ivis/node25.htm
  • Ontologie Eins Null
  • Ontology as a Branch of Philosophy

    1. 1. Ontology as a Branch of Philosophy Barry Smith
    2. 2. A brief history of ontology Aristotle (384 BC – 322 BC) Realist theory of categories Intelligible universals extending across all domains Central role of organisms Medieval scholastics: Aquinas, Scotus, Ockham, … (1200 – 1600) Aristotelianism as philosophia perennis Common panscientific ontology and controlled vocabulary (Latin) 2
    3. 3. A brief history of ontology Descartes (1596 – 1650) Sceptical doubt initiates subversion of metaphysics, rise of epistemology Central role of mind Dualism of mind and matter Kant (1724 – 1804) Reality is unknowable Metaphysics is impossible We can only know the quasi-fictional domains which we ourselves create 3
    4. 4. A brief history of ontology Brentano (1838 – 1917) Rediscovery of Aristotle Methods of philosophy and of science are one and the same Husserl (1859 – 1938) Inventor of formal ontology as a discipline distinct from formal logic Showed how philosophy and science had become detached from the ‘life world’ of ordinary experience 4
    5. 5. The Four Phases of Philosophy rapid practical scepticism mysticism progress interest 5
    6. 6. First CycleThales to Stoicism and Pyrrho, Neo-Pythagoreans,Aristotle Epicureanism Eclectics Neo-Platonists 6
    7. 7. Second Cycle up to Scotism Ockham, Lull,Aquinas Nominalists Nicholas of Cusa 7
    8. 8. Third CycleBacon, Rationalists Hume, Berkeley, KantLocke Reid German Idealism 8
    9. 9. A brief history of ontology Wittgenstein 1 (ca. 1910 – 1918) Author of Tractatus Bases ontology on formal logic in reductionistic atomism Vienna Circle (1922 – ca. 1938) Schlick, Neurath, Gödel, Carnap, Gustav Bergmann … Centrality of logic to philosophy Construction of philosophy from either physics or sensations as base 9
    10. 10. A brief history of ontology Wittgenstein 2 (ca. 1930 – 1951) Centrality of language and of language games Metaphysics = language goes on holiday British Ordinary Language philosophy Philosophical problems to be solved by the study of the workings of language Speech Act Theory (J. L. Austin, 1911- 1960) 10
    11. 11. A brief history of ontology Quine (ca. 1930 – 1951) Ontological commitment (study not: what there is, but: what sciences believe there is when logically formalized) Analytical metaphysics (from ca. 1980): Chisholm, Lewis, Armstrong, Fine, Lowe, … beginnings of a rediscovery of metaphysics as first philosophy What next? 11
    12. 12. Fourth Cycle (Continental) Brentano Husserl Heidegger Derrida andPolish School the French 12
    13. 13. Fourth Cycle (Analytical) Frege Vienna Circle Wittgenstein 2 RortyWittgenstein 1 Quine Russell 13
    14. 14. Each cycle begins with rediscovery of Aristotle and a new theoretical orientationFrom the 3rd cycle markedby invention of new disciplines3. Empirical natural science4. Psychology, logic 14
    15. 15. Fifth CycleAnalytical Metaphysics OntologyRediscovery of Aristotle 15
    16. 16. An example of a practical problemIncreasingly, publishers are exploring ways to tagscientific literature in ways designed to make theircontents more easily accessible to computersFor maximal effect, a single set of terms should beused for tagging all literature published in a givendomainHow do we select the set of terms (‘ontology’) foreach domain? 16
    17. 17. from: http://www.ploscompbiol.org/doi/pcbi.1000361 17
    18. 18. http://www.biocurator.org 18
    19. 19. 19
    20. 20. Most successful ontology venture thus far $100 mill. invested in literature and database curation using the Gene Ontology (GO) over 11 million annotations relating gene products (proteins) described in the UniProt, Ensembl and other databases to terms in the GO 20
    21. 21. GO provides a controlled system ofrepresentations for use in annotating data and literature that is • multi-species • multi-disciplinary • multi-granularity, from molecules to population 21
    22. 22. 22
    23. 23. The GO and its sister ontologies are structured representations of the domains of molecules, cells, diseases ... which can be used by researchers in many different disciplines who are focused on one and the same biological reality 23
    24. 24. The goal: virtual science • consistent (non-redundant) annotation • cumulative (additive) annotationyielding, by incremental steps, a virtualmap of the entirety of reality that isaccessible to computational reasoning 24
    25. 25. This goal is realizable if we have a common ontology framework data is retrievable data is comparable data is integratableonly to the degree that it is annotatedusing a common controlled vocabulary– compare the role of seconds,meters, kilograms … in unifyingscience 25
    26. 26. To achieve this end we have to engage in something like philosophy is this the right way to organize the top level of this portion of the GO? how does the top level of this ontology relate to the top levels of other, neighboring ontologies? 26
    27. 27. Aristotle’s MetaphysicsThe world is organized viatypes/universals/categories which arehierarchically organized 27
    28. 28. This holds, too, of the biological world 28
    29. 29. Porphyrian Hierarchy 29
    30. 30. Linnaean Hierarchy 30
    31. 31. From Species to Genera animal birdcanary 31
    32. 32. From Species to Genera has skin eats animal breathes moves has wings bird can fly has featherscanary can sing is yellow species-genus hierarchy as inference machine 32
    33. 33. From Species to Genera has skin eats animal breathes moves has wings has fins bird can fly fish can swim has feathers has gillscanary can sing is yellow 33
    34. 34. From Species to Genera has skin eats animal breathes moves has wings bird can fly has feathers X can singcanary is yellow species-genus hierarchy as inference machine 34
    35. 35. Question: Why are species-genus hierarchies good ways torepresent the world for purposesof reasoning?Answer: They capture the way theworld is (Aristotelian realism) 35
    36. 36. Transcription is_a biological processTranscription part_of gene expression 36
    37. 37. Species-genus trees can berepresented also as map-likepartitionsIf Aristotelian realism is right, thensuch partitions, when correctlybuilt are transparent to the realitybeyond 37
    38. 38. From Species to Genera animal birdcanary 38
    39. 39. From Species to Genera animal birdcanary 39
    40. 40. Alberti’s Grid c.1450 40
    41. 41. Ontologies: windows onthe universals in reality 41
    42. 42. as through a transparent grid Artist’s Grid 42
    43. 43. Species-Genera as Map/Partition animal bird fishcanary ostrich 43
    44. 44. species, substancegenera organism animal mammal cat frogsiameseinstances 44
    45. 45. Aristotle’s Metaphysics is focused onobjects (things, substances, organisms)The most important universals in hisontology are substance universals cow man rock planetwhich pertain to what a thing is at alltimes at which it exists 45
    46. 46. For Aristotle, the worldcontains also accidentswhich pertain to how a thing is atsome time at which it exists: red hot suntanned spinning= what holds of a substance per accidens 46
    47. 47. Accidents, too, instantiategenera and species Thus accidents, too, form trees of greater and lesser generality 47
    48. 48. Accidents: Species and instances quality color red scarlet R232, G54, B24this individual accident of redness (this token redness – here, now) 48
    49. 49. Nine Accidental Categories 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 49
    50. 50. Substances are the bearers of accidents hunger John = relations of inherence (one-sided existential dependence) 50
    51. 51. Aristotle 1.0an ontology recognizing: substance tokens accident tokens substance types accident types 51
    52. 52. Aristotle’s Ontological Square Substantial Accidental Second substance Second accident Universal man headache cat sun-tan ox dread First substance First accident Particular this man this headache this cat this sun-tan this ox this dread 52
    53. 53. Some philosophers accept only part of this four category ontology 53
    54. 54. Standard Predicate Logic – F(a), R(a,b) ... Substantial Accidental Attributes Universal F, G, R Individuals Particular a, b, c this, that 54
    55. 55. Bicategorial NominalismUniversal Substantial Accidental First substance First accidentParticular this man this headache this cat this sun-tan this ox this dread 55
    56. 56. Process MetaphysicsUniversal Substantial Accidental EventsParticular Processes “Everything is flux” 56
    57. 57. In fact however we need morethan the ontological squareNot everything in reality iseither a substance or anaccident 57
    58. 58. Positive and negative parts negative part or hole (not madepositive of matter)part(made of matter) 58
    59. 59. Shoes 59
    60. 60. Pipe 60
    61. 61. Niches, environments are holes 61
    62. 62. Places are holes 62
    63. 63. Places are holes 63
    64. 64. Nine Accidental Categories 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 64
    65. 65. PlacesFor Aristotle the place of a substance isthe interior boundary of the surroundingbody(for example the interior boundary of thesurrounding water where it meets a fish’sskin)For holes, we need an extension ofAristotle’s metaphysics 65
    66. 66. A hole in the groundSolid physical boundaries at the floorand wallsbut with a lid that is not made of matter: hole 66
    67. 67. Holes involve two kinds of boundariesbona fide boundaries which existindependently of our demarcating actsfiat boundaries which exist only becausewe put them there 67
    68. 68. Examplesof bona fide boundaries:an animal’s skin, the surface of the planetof fiat boundaries:the boundaries of postal districts and census tracts 68
    69. 69. Mountainbona fide upper boundarieswith a fiat base: 69
    70. 70. where does the mountain start ? ... a mountain is not a substance 70
    71. 71. Cerebral Cortex 71
    72. 72. Aristotle 1.5an ontology of substances + accidents + holes (and other entities not made of matter) + fiat and bona fide boundaries + artefacts and environments 72
    73. 73. QuestionHow do those parts and dimensions ofreality which we encounter in our everydayexperience relate to those parts anddimensions of reality which are studied byscience? 73
    74. 74. Aristotle 2010scientific realism coupled withrealism about the everyday world 74
    75. 75. animal Universe/Periodic Table fish folk biology bird canary ostrichpartition of DNA space 75
    76. 76. animal Universe/Periodic Table fish bird canary ostrichboth are transparentpartitions of one and thesame reality 76
    77. 77. An organism is a totality of atomsAn organism is a totality of moleculesAn organism is a totality of cellsAn organism is a single unitary substance... all of these express veridical partitions 77
    78. 78. Multiple transparent partitionsat different levels of granularityoperating with species-genus hierarchiesand with an ontology of substances andaccidents along the lines described byAristotlesubstances and accidents reappear in themicroscopic and macroscopic worlds of e.g.of chemistry and evolutionary biology 78
    79. 79. we do not assertthat every level of granularity is structured in substance-accident form -- perhaps there are pure process levels, perhaps there are levels structured as fields 79
    80. 80. Perspectivalism PerspectivalismDifferent partitions may represent cutsthrough the same reality which areskew to each otherNot all need be structured in substance-accident terms – perhaps there arepure process levels, perhaps there arelevels structured as fields 80
    81. 81. Periodic Table 81
    82. 82. 82
    83. 83. Scientific partitions like the PeriodicTable or the Gene Ontologyare transparent to the hierarchical order ofan associated domain of objectsthey capture reality at different levels ofgranularitycellular constituents are visible to the GO,molecular constituents not 83
    84. 84. PerspectivalismPerspectivalismDifferent partitions may representcuts through the same reality whichare skew to each otherDifferent partitions may capturereality in ways which involvedifferent degrees of vagueness 84
    85. 85. From Species to Genera has skin eats animal breathes moves has wings has fins bird can fly fish can swim has feathers has gillscanary can sing is yellow 85
    86. 86. From Species to Genera has skin eats animal breathes moves has wings has fins bird can fly fish can swim has feathers has gills can sing y has long thin legscanary ostrich is tall is yellow can‘t fly 86
    87. 87. From Species to Genera has skin eats animal breathes moves has wings has fins bird can fly fish can swim has feathers has gills can sing y has long thin legscanary ostrich is tall is yellow can’t fly 87
    88. 88. Theory of vaguenessHow can -basedconceptualizations be transparent,if the world is shaped like this ? 88
    89. 89. Observe that no such problemsarise for the closed worldsconstructed in informationsystemshierarchies as reasoning tools work verywell for the closed worlds of databaseengineers 89
    90. 90. whether a file is in a given folder on yourhard-drive is completely determinate: 90
    91. 91. Dewey Decimal Classification 91
    92. 92. Dewey Decimal Classification (Detail) 92
    93. 93. No borderline cases in theclosed world of a databaseEvery book is assigned a determinateDewey Classification Number at birth 111.560xxx this yields a classification that is completely crisp 93
    94. 94. ... and always up-to-dateTo be a book = to have a referencenumber in the Catalogue SystemEach of the ontologies produced byontological engineers deals with objectswhich are constructed (Kant would say“constituted”) by the database itself 94
    95. 95. Kant 95
    96. 96. Sharpness of database realityvs. vagueness of flesh andblood realityHow to deal with the problemof vagueness of our representations?How to create adequate representationsbeyond the quasi-Kantian realm of databaseengineers 96
    97. 97. Kantian ConstructivismThere are no species-genus hierarchies inreality unless we put them thereThe world – insofar as it is accessible tous through our concepts at all – is a closedsystem tailored by us to fit those concepts 97
    98. 98. Kantianism seems to workvery well for the closed worldsof database environmentsThere Midas-touch epistemology isappropriateIf our database recognizes only twogenders, then the world represented inthe database is a world in which thereare only two genders 98
    99. 99. hard vs. soft categoriesKantianism: we constitute/shape(empirical) reality in such a way that itcorresponds to our categoriesAristotelianism: reality in itself ismessy, but our categories fitnonetheless 99
    100. 100. For Aristotelianswhen we apply general terms to reality weare aware that we may have to deal withan opposition... between standard or focal orprototypical instances of thecorresponding universals... and non-standard or ‘fringe’ instances 100
    101. 101. Natural categories have borderline cases sparrow ostrich birds 101
    102. 102. ... they have a kernel/penumbra structure penumbra of borderline cases kernel of focal instances 102
    103. 103. Species Genera as Tree animal bird fishcanary ostrich 103
    104. 104. Species-Genera as Map/Partition animal bird fishcanary ostrich 104
    105. 105. animal fish birdcanary ostrich 105
    106. 106. Coarse-grained Partitionwhat happens whena fringe instance arises ? 106
    107. 107. Aristotle 2010you seek to find a finer grained partitionwhich will recognize the phenomenon inquestion and allow an explanation ofwhy it deviates from the prototype 107
    108. 108. 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 108
    109. 109. Kantianismeach partition gives only a partial view (nocomplete map) of any reality beyondand thus it gives a distorted view– we can only really know what weourselves have constructed 109
    110. 110. For the Aristotelian, there are two sorts of partitions: those which relate merely to a created, surrogate world (Library of Congress Catalog) those which are transparent to some independent reality beyond (Gene Ontology) 110
    111. 111. Concepts vs. categorieson the Kantian reading species areconcepts, which we bring to realityon the Aristotelian reading the world itselfexhibits a species-genus structureindependently of how we conceive it andwe do our best to map this structure in ourrepresentations 111
    112. 112. Basic Formal Ontology (BFO) Occurrent Continuant (Process)Independent Dependent Continuant Continuant..... ..... ........ 112