1. New Foundations for Social Ontology Barry Smith http://ontology.buffalo.edu/smith 1

2. We will be able to use ontologies to help us share data are ontologically coherent (created under adult supervision) and logically coherent and computationally tractable and work well together – evolve together – created according to the tested rules 2

3. A new approach prospective standardization based on objective measures of what works bring together selected groups to agree on and commit to good terminology / annotation habits (traffic laws) preemptively 3

4. Compare science 1.scientific theories must be common resources (cannot be bought or sold) 2.they must use open publishing venues 3.they must constantly evolve to reflect results of scientific experiments (“evidence-based”) 4.must be synchronized –use common SI system of units –common mathematical theories (built by adults) 4

5. for science create an evolutionary path towards improvement, of the sort we find in science a collaborative, community effort to ensure buy-in with rewards for participation good versioning principles to ensure legacy annotation efforts not wasted Requirements 5

6. for science Create a consensus core of interoperable domain ontologies starting with low hanging fruit and working outwards from there built and validated by trained experts backed by persons of influence in different communities 6

7. This solution is already being implemented in the domain of biomedicine 7

8. Uses of ‘ontology’ in PubMed abstracts 8

9. By far the most successful: GO (Gene Ontology) 9

10. a family of interoperable gold standard biomedical reference ontologies, based on the Gene Ontology http://obofoundry.org The OBO Foundry 10

11. RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) The Open Biomedical Ontologies (OBO) Foundry 11

12. CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Organism-Level Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Cellular Process (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) OBO Foundry ontology modules GRANULARITY RELATION TO TIME 12

13. Central principle of the OBO Foundry: ontological modularity division of labor division of expertise division of authority no mapping problem additivity of annotations no silo effect – always one ontology for every need creates tested guidelines (traffic laws) for those with new ontology needs 13

14. Obstacles to the realization of ontology modularity based on coherent traffic laws of the sort we find in science Computer scientists are teaching people ontology tools Computer engineers have an interest in multiple new ontologies Every Tuesday a new ontology of wheat 14

15. The result: Paris has_temperature 62 o Mohammed is_a string Amount of money is_a integer Currency has_unit $ Nuclear weapon is_a concept 15

16. ontologies for ‘agent’ 16

17. 17

18. SUMO Contract = def. Attribute that applies to Propositions where something is promised in return, i.e. a reciprocal promise.Attribute Proposition 18

19. Cyc Contract =def. a collection of agreements [whereby] each sentence is a legal agreement in which two or more agreeing agents promise to do (or not to do) something. There are legal consequences to breaking the promises made in a contract 19

20. Legal Ontology of Contract Formation http://www.dit.unitn.it/~pavel/cando/Pictures/Posters/Mull en.pdf 20

21. Legal Ontology of Contract Formation http://www.dit.unitn.it/~pavel/cando/Pictures/Posters/Mull en.pdf 21

22. http://www.mit.edu/~bgrosof/paps/contracts-with-exceptions-workshop.pdf SweetDeal rule-based approach to representation of business contracts 22

23. http://www.mit.edu/~bgrosof/paps/contracts-with-exceptions-workshop.pdf SweetDeal rule-based approach to representation of business contracts 23

24. Pervasive Semantic Web 24

25. What we need 1 (adults) a thoroughly tested, mandated, common top-level ontology to enable minimal ontology interoperability thoroughly tested, mandated domain ontologies built and maintained recognized by domain experts 25

26. What we need 2 (training) Professional training for ontologists to teach people to CREATE ONTOLOGY CONTENT to teach people to USE ONTOLOGY CONTENT 26

27. What we need 3 (institutions) institutions for ontology standardization – counterparts of the authority structure maintained by Linux or by the SI System of Units or the IUPAC chemical nomenclature organization (W3C does not see what is needed for advancement of ontology towards coherence and consistency) 27

28. What we need 4 (standards) Standards governing rules for ontology development, versioning, modularity ensuring interoperability Authorities able to apply these rules, and ensure filling in of gaps by experts sustainability 28

29. What we need 6 (Darwinian struggle for survival) ontology evaluation with teeth if ontology (science) is to be born, ontologies must die 29

30. Ontology needs to become more like a science basis in evidence established results – authoritative ontologies* expert peer review credit for good ontology work 30

31. Peer review evaluation process Required where the quality of inputs cannot be evaluated mechanically -- journal articles -- research proposals -- people (for career promotion in universities …) 31

32. Treat ontologies like publications This is happening already with databases: Nature Signaling Nature Pathway Interactions Nature Ontologies ? Ontology peer review methodology being tested within the OBO Foundry 32

33. Peer review assessment tasks Is the ontology consistent with the rules (on modularity, …) ? Does the ontology provide adequate coverage of its defined domain? To what level is inferencing supported in the ontology relations structure? Does the ontology interoperate with other ontologies in the system 33

34. Is the ontology being developed collaboratively through the engagement and participation of relevant domain stakeholders and developers of neighboring ontologies? Does the ontology have a tracker for submissions of new terms and notification of errors? Does the ontology have a help desk which has prompt response times? 34

35. Is the ontology syntactical correct Is a URI assigned to each term of the ontology? Does the URI point to required metadata for this term (including natural language and formal definitions). Are all identifiers and preferred terms unique Are all asserted subclass relations correct in light of the intended interpretation 35

36. Perhaps the ontology of law needs silos? But if we are to use ontologies as a rigorous means of comparing and integrating legal systems and associated data, then we need a robust common ontology framework -- a common top-level ontology -- a common set of ontology relations -- common (mid-level) domain ontologies 36

37. http://code.google.com/p/information- artifact-ontology/ Information Artifact Ontology One domain ontology with which an ontology of legal entities must cohere: 37

38. Basic Formal Ontology (BFO) Continuant Occurrent process Independent Continuant thing Dependent Continuant quality, role, function …................ 38

39. Blinding Flash of the Obvious Continuant Occurrent process Independent Continuant thing Dependent Continuant quality................ quality depends on bearer 39

40. Information entities are relative to provenance and to processors in a way in which types are not 40

41. What is a datum? Continuant Occurrent process Independent Continuant laptop, book Dependent Continuant quality................ datum: a pattern in some medium with a certain kind of provenance 41

42. Continuant Occurrent Independent Continuant Dependent Continuant................ Information Entity Action creating a datum 42

43. Generically Dependent Continuants Generically Dependent Continuant Information Entity Sequence if one bearer ceases to exist, then the entity can survive, because there are other bearers (copyability) the pdf file on this laptop the DNA (sequence) in that chromosome 43

44. Generically Dependent Continuants Generically Dependent Continuant Information Artifact Gene Sequence.pdf file.doc file instances 44

45. Transcriptomics (MIAME Working Group) Proteomics (Proteomics Standards Initiative) Metabolomics (Metabolomics Standards Initiative) Genomics and Metagenomics (Genomic Standards Consortium) In Situ Hybridization and Immunohistochemistry (MISFISHIE Working Group) Phylogenetics (Phylogenetics Community) RNA Interference (RNAi Community) Toxicogenomics (Toxicogenomics WG) Environmental Genomics (Environmental Genomics WG) Nutrigenomics (Nutrigenomics WG) Flow Cytometry (Flow Cytometry Community) IAO adopted, and being violently tested, inter alia, by: 45

46. Information Entity (science) ‘information’ – mass noun (Shannon and Weaver) ‘information entity’ – count noun (Information Ontology) Information entities are, roughly: artifacts in the realm of qualities (patterns) 46

47. Information Entity (science) protocol database theory ontology gene list publication result... 47

48. Information Entity (labeling) serial number batch number grant number person number name address email address URL... 48

49. Type or instance Continuant Occurrent (Process) Independent Continuant human being, protocol document Dependent Continuant pattern of ink marks Applying the protocol Side-Effect …................... 49

50. Continuant Occurrent Independent Continuant Dependent Continuant................ Information Entity Action creating a datum 50

51. type: human being Instance: Leon Tolstoy type: novel Instance: War and Peace type: book Instance: this copy of War and Peace Types and instances 51

52. 52

53. Is the Coca-Cola trademark a type or an instance? If the Coca-Cola trademark were a type, and the copies on my laptop and on your laptop instances, then there would be many Coca-Cola trademarks Hence the Coca-Cola trademark is an instance What is a trademark? 53

54. Is War and Peace a type or an instance? If War and Peace were a type, and the copies of War and Peace in my library and in your library were instances, then there would be many War(s) and Peaces. Hence War and Peace is an instance. What is a work of literature? 54

55. There can be two copies of the US Declaration of Independence There cannot be two US Declarations of Independence There cannot be subtypes of the US Declaration of Independence There are not two Declarations of Independence 55

56. Rule for types Their names are pluralizable There can be three people There cannot be three Condoleezza Rices Information Entities = entities which can exist in many perfect copies 56

57. Specific dependence Continuant Occurrent process Independent Continuant thing Dependent Continuant quality................ headache depends on human being 57

58. Generically Dependent Continuants Generically Dependent Continuant Information Entity Sequence if one bearer ceases to exist, then the entity can survive, because there are other bearers (copyability) the pdf file on my laptop the DNA (sequence) in this chromosome 58

59. are realized through being concretized in specifically dependent continuants (the plan in your head, the protocol being realized by your research team) Generically dependent continuants 59

60. they have a different kind of provenance ◦ Aspirin as product of Bayer GmbH ◦ aspirin as molecular structure Generically dependent continuants are distinct from types 60

61. Generically Dependent Continuants Generically Dependent Continuant Information Entity Sequence.pdf file.doc file instances 61

62. are concretized in specifically dependent continuants Beethoven’s 9th Symphony is concretized in the pattern of ink marks which make up this score in my hand Generically dependent continuants 62

63. do not require specific media (paper, silicon, neuron …) Generically dependent continuants 63

64. Realizable Dependent Continuants Specifically Dependent Continuant Quality, Pattern Realizable Dependent Continuant inert ert Occurrent 64

65. Examples performance of a symphony projection of a film utterance of a sentence application of a therapy course of a disease increase of temperature Occurrent Realizable Dependent Continuant 65

66. Continuant Occurrent Independent Continuant Specifically Dependent Continuant QualityDisposition Realization Role Realizable Dependent Continuant Generically Dependent Continuant 66

67. A violinist reads the score of Beethoven’s 9th Symphony and a concretization of the Symphony is created in his mind (something like a plan) In playing he realizes this plan, thereby generating a performance of the Symphony Realizable Dependent Continuants are always specifically dependent 67

68. Nature Protocols vs. The protocol McDoe has been following in this project since March Realizable Dependent Continuants are always specifically dependent 68

69. McDoe reads the protocol as published and a concretization of the protocol is created in his mind (something like a plan) In his laboratory work he realizes this plan, thereby generating an experiment Realizable Dependent Continuants are always specifically dependent 69

70. Informational Entity (law) license permission contract regulation... 70

71. Open Source Licenses Open source licenses define the privileges and restrictions a licensor must follow in order to use, modify or redistribute the open source software. Examples include Apache License, BSD license, GNU General Public License,...Apache LicenseBSD licenseGNU General Public License The proliferation of open source licenses is one of the few negative aspects of the open source movement because it is often difficult to understand the legal implications of the differences between licenses. (Wikipedia) 71

72. By following the strategy of the Gene Ontology Examine the instances in reality – laptops, labels, actions of signing contracts – and their interrelations Distinguish license template from license (correctly filled-in) How to create a common representation of the entities in the domain of contracts and licensing? 72

73. All terms in an ontology must have instances in reality Ontologies must be anchored to reality through these instances We anchor the ontology of information entities through human acts of using language, through documents, through acts of entering data into a registry... Basic rule of evidence-based ontology 73

74. Open Source Licenses Open source license as generically dependent continuant (compare: protocol in Nature Protocols) The license signed by John and Jim, a specifically dependent continuant whose bearer is (say) a specific piece of paper The former is a concretization of the latter 74