1. Ontological Engineering Barry Smith http://ontology.buffalo.edu Computers and Information in Engineering Conference, Buffalo August 19, 2014 1

3. GO is amazingly successful in overcoming problems of balkanization, especially for retrieval of data but it covers only generic biological entities of three sorts: – cellular components – molecular functions – biological processes and it does not provide representations of diseases, symptoms, anatomy, pathways, … 3

4. 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) Original OBO Foundry ontologies (Gene Ontology in yellow) 4

5. 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) Environment Ontology (EnvO) Environments 5

6. Anatomy Ontology (FMA*, CARO) Environment Ontology (ENVO) Infectious Disease Ontology (IDO*) Biological Process Ontology (GO*) Cell Ontology (CL) Cellular Component Ontology (FMA*, GO*) Phenotypic Quality Ontology (PATO) Subcellular Anatomy Ontology (SAO) Sequence Ontology (SO*) Molecular Function (GO*) Protein Ontology (PRO*) top level mid-level domain level Information Artifact Ontology (IAO) Ontology for Biomedical Investigations (OBI) Spatial Ontology (BSPO) Basic Formal Ontology (BFO) domain ontologies created by specialization from BFO

7. Basic Formal Ontology (BFO) core nodes domain ontologies created by specialization from BFO Independent continuants Dependent continuants Occurrents Classes Object types Attribute types Process types Particulars Individual objects Individual attributes Individual processes

8. BFO 2.0 8

9. – CHEBI: Chemical Entities of Biological Interest – GO: Gene Ontology – OBI: Ontology for Biomedical Investigations – PATO: Phenotypic Quality Ontology – PO: Plant Ontology – PATO: Phenotypic Quality Ontology – PRO: Protein Ontology – XAO: Xenopus Anatomy Ontology – ZFA: Zebrafish Anatomy Ontology http://obofoundry.org 9 http://www.ifomis.org/bfo/

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11. OBO Foundry approach extended into other domains 11 NIF StandardNeuroscience Information Framework IDO ConsortiumInfectious Disease Ontology cROPCommon Reference Ontologies for Plants MilPortal.orgMilitary Ontology AIRS Ontology SuiteActionable Intelligence Retrieval System

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13. MilPortal http://milportal.ncor.buffalo.edu/ontologies 13

14. 14

15. How classify this? 15

16. or this? 16

17. http://bioportal.bioontology.org/ontologies/49078 17 The Emotion Ontology

18. need link to a physiology ontology 18 ‘physiological response to emotion’

19. 19 ‘emotion process’

20. 20

21. 21 BFO als standard upper-level Ontologie Wie Ontologien die wissenschaftliche Forschung unterstützen Warum wissenschaftliche Ontologien zusammenarbeiten müssen Basic Formal Ontology (BFO): die Vorteil der Koordination Benützer von BFO Kontinuanten, Okkurrenten, Realisierungen Arten der Abhängigkeit

22. 22 The idea of ontological realism Before we build a data model we need to look at the reality we are trying to represent (= let’s look at the best scientific theory we have of this reality) Let’s constrain our data models so that our databases are veridical representations of the world outside

23. 23 Scientific ontologies have special features Every term in a scientific ontology must be such that the developers of the ontology believe it to refer to some entity* in reality on the basis of the best current evidence *in first approximation: instances of a type

24. located near Latrine Well ‘VT 334 569’ Distance Measurement Result Village Name ‘Khanabad Village’ Village is_a instance_ of Geopolitical Entity Spatial Region Geographic Coordinates Set designates instance_of located in instance_of has location designates has location instance_of ’16 meters’ instance_of measurement_of 24 Universals and Instances (from Bill Mandrick)

25. 25 For science, and thus for scientific ontologies, it is generalizations that are of prime important = universals, types, kinds, species

26. 26 For scientific ontologies reusability, openness is crucial intelligibility to humans is crucial revisability is crucial there is always an open world assumption testability is crucial compatibility with neighboring scientific ontologies is crucial  it should not be too easy to add new terms to an ontology

27. 27 For scientific ontologies the issue of how the ontology will be used is not a factor relevant for determining how entities are treated by the ontology If this decision is made to reflect specific, local practical needs, this will thwart reusability of the data the ontology is used to annotate

28. BFO A simple top-level ontology to support information integration in scientific research Defining a framework that will help to ensure consistency and non-redundancy of the ontologies created in its terms 28

29. Three Fundamental Dichotomies Continuant vs. occurrent Dependent vs. independent Type vs. instance http://ontology.buffalo.edu/bfo/ 29

30. Continuant thing, quality … Occurrent process, event 30

31. depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality quality depends on bearer 31

32. depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality, … event depends on participant 32

33. instance_of Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality................ types instances 33

34. depends_on Continuant Occurrent process Independent Continuant thing Dependent Continuant quality................ temperature depends on bearer 34

35. 3 kinds of (binary) relations Between types human is_a mammal human heart part_of human Between an instance and a type this human instance_of the type human this human allergic_to the type tamiflu Between instances Mary’s heart part_of Mary Mary’s aorta connected_to Mary’s heart 35

36. Clark et al., 2005 part_of is_a Definitions of relations 36 Barry Smith, et al., “Relations in Biomedical Ontologies”, Genome Biology 2005, 6 (5), R46.

37. Type-level relations presuppose the underlying instance-level relations A part_of B =def. All instances of A are instance-level-parts-of some instance of B e.g. human heart part_of human A has_participant B =def. All instances of A have an instance of B as instance-level participant e.g. cell binding has_participant cell 37

38. Blinding Flash of the Obvious Continuant Occurrent (Process, Event) Independent Continuant Dependent Continuant How to create an ontology from the top down 38

39. Example: The Cell Ontology

40. Benefits of coordination No need to reinvent the wheel Can profit from lessons learned through mistakes made by others Can more easily reuse what is made by others Can more easily inspect and criticize results of others’ work (PATO) Leads to innovations (e.g. Mireot) in strategies for combining ontologies 40

41. Users of BFO PharmaOntology (W3C HCLS SIG) MediCognos / Microsoft Healthvault Cleveland Clinic Semantic Database in Cardiothoracic Surgery Major Histocompatibility Complex (MHC) Ontology (NIAID) Neuroscience Information Framework Standard (NIFSTD) and Constituent Ontologies 41

42. Users of BFO Interdisciplinary Prostate Ontology (IPO) Nanoparticle Ontology (NPO): Ontology for Cancer Nanotechnology Research Neural Electromagnetic Ontologies (NEMO) ChemAxiom – Ontology for Chemistry Ontology for Risks Against Patient Safety (RAPS/REMINE) (EU FP7) IDO Infectious Disease Ontology (NIAID) 42

43. Users of BFO National Cancer Institute Biomedical Grid Terminology (BiomedGT) US Army Universal Core Semantic Layer (UCore SL) US Army Biometrics Ontology US Army Command and Control Ontology Ontology for General Medical Science (OGMS) 43

44. Infectious Disease Ontology Consortium MITRE, Mount Sinai, UTSouthwestern – Influenza IMBB/VectorBase – Vector borne diseases (A. gambiae, A. aegypti, I. scapularis, C. pipiens, P. humanus) Colorado State University – Dengue Fever Duke University – Tuberculosis, Staph. aureus, HIV Case Western Reserve – Infective Endocarditis University of Michigan – Brucilosis 44

45. – GO Gene Ontology – CL Cell Ontology – SO Sequence Ontology – ChEBI Chemical Ontology – PATO Phenotype (Quality) Ontology – FMA Foundational Model of Anatomy – ChEBI Chemical Entities of Biological Interest – PRO Protein Ontology – Plant Ontology – Environment Ontology – Ontology for Biomedical Investigations – RNA Ontology OBO Open Biomedical Ontologies 45

46. 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 46

47. maintained by Werner Ceusters, Buffalo Pierre Grenon, Open University Chris Mungall, Berkeley Fabian Neuhaus, NIST Holger Stenzhorn, IFOMIS, Saarland University Alan Ruttenberg, Science Commons plus 103 other members of BFO Discussion Group: http://groups.google.com/group/bfo-discuss?

48. inspired by Aristotle Husserl Roman Ingarden Ingvar Johansson Kevin Mulligan, University of Geneva Cornelius Rosse Peter Simons, Trinity College, Dublin Wittgenstein’s Tractatus (picture theory of language) Wolfgang Degen, Nicola Guarino, Patrick Hayes

49. Blinding Flash of the Obvious Continuant Occurrent (Process, Event) Independent Continuant Dependent Continuant How to create an ontology from the top down 49

50. Specifically Dependent Continuant Red color of my skin YouMe Accidens non migrat de subjecto in subjectum. Accidents do not migrate from one substance to another 50 Red color of your skin depends_on

51. Continuant Independent Continuant Dependent Continuant.......... Non-realizable Dependent Continuant (quality) Realizable Dependent Continuant (function, role, disposition) 51

52. Realizable dependent continuants plan function role disposition capability tendency continuants 52

53. Their realizations execution expression exercise realization application course occurrents 53

54. Continuant Independent Continuant Dependent Continuant.......... Non-realizable Dependent Continuant (quality) Realizable Dependent Continuant (function, role, disposition) 54

55. realization depends_on realizable Continuant Occurrent Independent Continuant bearer Dependent Continuant disposition................ Process of realization 55

56. Specific Dependence on the instance level a depends_on b =def. a is necessarily such that if b ceases to exist than a ceases to exist on the type level A specifically_depends_on B =def. for every instance a of A, there is some instance b of B such that a depends_on b. 56

57. depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality................ temperature depends on bearer 57

58. 58 The (Aristotelian) Ontological Sextet SubstancesQuality entitiesProcesses Universals Substance- universals Quality- universals Process- universals Particulars Individual Substances Quality- instances (Tropes…) Process- instances

60. Specifically dependent continuants the quality of whiteness of this cheese your role as lecturer the disposition of this patient to experience diarrhea 60

61. the particular case of redness (of a particular fly eye) the universal red instantiates an instance of an eye (in a particular fly) the universal eye instantiates depends on 61

62. the particular case of redness (of a particular fly eye) red instantiates an instance of an eye (in a particular fly) eye instantiates depends on coloranatomical structure is_a 62

63. depends_on Continuant Occurrent process Independent Continuant thing Dependent Continuant quality................ temperature depends on bearer 63

64. Specifically Dependent Continuants Specifically Dependent Continuant Quality, Pattern Realizable Dependent Continuant if the bearer ceases to exist, then its quality, function, role ceases to exist the color of my skin the function of my heart to pump blood my weight 64

65. 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 65

66. 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) rationale of OBO Foundry coverage GRANULARITY RELATION TO TIME 66

67. Continuant Independent Continuant Specifically Dependent Continuant.......... Quality Realizable Dependent Continuant (function, role, disposition) 67

68. Specific Dependence on the instance level a depends_on b =def. a is necessarily such that if b ceases to exist than a ceases to exist on the type level A specifically_depends_on B =def. for every instance a of A, there is some instance b of B such that a depends_on b. 68

69. Generically Dependent Continuants Generically Dependent Continuant Information Object Gene 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 69

70. Continuant Independent Continuant Specifically Dependent Continuant.......... Quality Realizable Dependent Continuant (function, role, disposition) 70

71. Realizable dependent continuants plan function role disposition capability tendency continuants 71

72. Their realizations execution expression exercise realization application course occurrents 72

73. Continuant Occurrent Independent Continuant Specifically Dependent Continuant Quality Disposition Functioning Function Generically Dependent Continuant Realizable Role Information Artifact Sequence…

74. IAO IAO: The Information Artifact Ontology, developed by scientific researchers as a vehicle for annotating data about measurement results, publications, protocols, databases, consent forms, licenses in a way that will allow discovery, integration and analysis Two kinds of data about data: – 1. what are the data about  Domain Ontologies – 2. how the data are packaged (collected, presented, formatted, stored)  IAO Ontologies