2. Historical Introduction to Ontologies Barry Smith

3. A brief history of ontology Aristotle: Ontology is first philosophy Realist theory of categories based on substances and accidents universals and particulars Epistemological optimism 2

4. Porphyrian Hierarchy 3

5. Linnaean Hierarchy 4

6. Epistemological pessimism Descartes: Sceptical doubt, epistemology is first philosophy, we can only know our own minds Kant: Reality in itself is unknowable; all we can ever know is our own concepts 5

7. The 20th Century Frege, Russell, Wittgenstein invention of first-order logic Logic is first philosophy Vienna Circle (1922 – 1938) Schlick, Neurath, Gödel, Carnap... “Universal science” Joseph Woodger, The Axiomatic Method in Biology (1937) 6

8. Primitive classesPrimitive relations cell male gamete female gamete whole organism organized unity genetic property part of earlier than derives by division or fusion from environment of primitive classes and relations in Woodger 7

9. sample page from Woodger 8

10. Analytical metaphysics Quine Ontological commitment (study not: what there is, but: what sciences believe there is when logically formalized) Nominalism: no universals or types, just generic predicates Analytical metaphysics (from ca. 1980): Chisholm, Armstrong, Fine, Lowe, … rediscovery of metaphysics as first philosophy Realist theory of universals 9

11. Applied Ontology, 5 (2010), 79–108 10

12. 11

13. Lord and Stevens “There are now over 60 ontologies in active use, increasingly developed as large, international collaborations. There are, however, many opinions on how ontologies should be authored... Recently, a common opinion has been the “realist” approach that places restrictions upon the style of modelling considered to be appropriate. 12

14. Lord and Stevens ‘... realism appears to be over-simplistic which, perversely, results in overly complex ontological models. We suggest that it is impossible to avoid compromise in modelling ontology; a clearer understanding of these compromises will better enable appropriate modelling...” 13

15. Two methodologies Logical conceptualism (Gary Merrill, Phil Lord, Robert Stevens,...) using received FOL, or OWL, each group should formalize the sentences they need, using the attributes they need (‘tolerance’), and then coordinate later to resolve forking problems Ontological realism (OBO Foundry) prospective standardization based on something like Basic Formal Ontology 14

16. Argument in favor of tolerance Scientists need flexibility For any proposed top-level ontological axiom – for example that the world is divided into continuants and occurrents – there are entrenched views both pro and contra. 15

17. Integrity is assured because users of OBO Foundry ontologies are focused on one and the same biological reality Take care of flexibility through: constant updates competing consortia user interfaces / views application ontologies built on a common core of reference ontologies Arguments against tolerance : 1. the need to prevent forking. 16

18. The lessons of the GO and the FMA Arguments against tolerance : 2. secondary uses. 17

19. Uses of ‘ontology’ in PubMed abstracts 18

20. By far the most successful: GO (Gene Ontology) 19

21. Hierarchical view representing relations between represented types 20

22. Most successful ontology venture thus far $100 mill. invested in literature and database curation using the Gene Ontology (GO) based on the idea of annotation over 11 million annotations relating gene products (proteins) described in the UniProt, Ensembl and other databases to terms in the GO multiple secondary uses – because the ontology was not built to meet one specific set of requirements 21

23. GO provides a controlled system of terms for use in annotating (describing, tagging) data multi-species, multi-disciplinary, open source contributing to the cumulativity of scientific results obtained by distinct research communities compare use of kilograms, meters, seconds in formulating experimental results 22

24. Sample Gene Array Data 23

25. where in the cell ? what kind of molecular function ? semantic annotation of data what kind of biological process? 24

26. natural language labels to make the data cognitively accessible to human beings 25

27. compare: legends for maps 26

28. compare: legends for diagrams 27

29. ontologies are legends for data 28

30. compare: legends for maps 29

31. ontologies are legends for images 30

32. what lesion ? what brain function ? 31

33. ontologies are legends for databases MouseEcotope GlyProt DiabetInGene GluChem sphingolipid transporter activity 32

34. annotation using common ontologies yields integration of databases MouseEcotope GlyProt DiabetInGene GluChem Holliday junction helicase complex 33

35. annotation using common ontologies can support comparison of data 34

36. annotation with Gene Ontology supports reusability of data supports search of data by humans supports comparison of data supports aggregation of data supports reasoning with data by humans and machines 35

37. 36

38. The goal: virtual science consistent (non-redundant) annotation cumulative (additive) annotation yielding, by incremental steps, a virtual map of the entirety of reality that is accessible to computational reasoning 37

39. This goal is realizable if we have a common ontology framework data is retrievable data is comparable data is integratable only to the degree that it is annotated using a common controlled vocabulary – compare the role of seconds, meters, kilograms … in unifying science 38

40. 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? 39

41. Strategy for doing this see the world as organized via types/universals/categories which are hierarchically organized and in relation to which statements can be formulated which are universally true of all instances: cell membrane part_of cell 40

42. 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 part_of is_a Foundational Model of Anatomy Ontology 41

43. siamese mammal cat organism substance species, genera animal instances frog 42

44. Aristotle’s metaphysics is focused on objects (things, substances, organisms) The most important universals in his ontology are substance universals cow man rock planet which pertain to what a thing is at all times at which it exists Substance universals form trees of greater and lesser generality 43

45. For Aristotle, the world contains also accidents which pertain to how a thing is at some time at which it exists: = what holds of a substance per accidens red hot suntanned spinning 44

46. Accidents, too, instantiate genera and species Thus accidents, too, form trees of greater and lesser generality 45

47. Accidents: Species and instances this individual accident of redness (this token redness – here, now) quality color red scarlet R232, G54, B24 46

48. = relations of inherence (one-sided existential dependence) John hunger Substances are the bearers of accidents 47

49. Aristotle’s Ontological Square SubstantialAccidental Second substance man cat ox Second accident headache sun-tan dread First substance this man this cat this ox First accident this headache this sun-tan this dread Universal Particular 48

50. In fact however we need more than the ontological square Not everything in reality is either a substance or an accident 49

51. Positive and negative parts positive part negative part or hole (made of matter) (not made of matter) 50

52. Different kinds of holes 51

53. Cerebral Cortex Different kinds of boundaries 52

54. Different levels of granularity 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 of one and the same reality 53

55. Beyond Aristotle an ontology of substances processes qualities, functions, roles + holes, cavities + fiat and bona fide boundaries +... information artifacts + multiple granularities 54

56. Ontology requires multiple transparent partitions at different levels of granularity operating with species-genus hierarchies and with an ontology of substances and accidents along the lines described by Aristotle substances and accidents reappear in the microscopic and macroscopic worlds of e.g. of chemistry and evolutionary biology 55

57. Periodic Table 56

58. 57