1. Lecture 3 BFO: A Standard Upper Level Ontology

2. 2 BFO als standard upper-level Ontologie Introduces Basic Formal Ontology (BFO) Shows how BFO is extended by the Information Artifact Ontology (controlled vocabulary for describing diagrams, images, documents, data, …)

3. 3 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

4. 4 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

5. 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 5 Universals and Instances (from Bill Mandrick)

6. 6 For science, and thus for scientific ontologies, it is generalizations that are of prime important = universals, types, kinds, species

7. 7 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

8. 8 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

9. 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 9

10. Three Fundamental Dichotomies Continuant vs. occurrent Dependent vs. independent Type vs. instance http://ontology.buffalo.edu/bfo/ 10

11. Continuant thing, quality … Occurrent process, event 11

12. depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality quality depends on bearer 12

13. depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality, … event depends on participant 13

14. instance_of Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality................ types instances 14

15. depends_on Continuant Occurrent process Independent Continuant thing Dependent Continuant quality................ temperature depends on bearer 15

16. 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 16

17. Clark et al., 2005 part_of is_a Definitions of relations 17 Barry Smith, et al., “Relations in Biomedical Ontologies”, Genome Biology 2005, 6 (5), R46.

18. 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 18

19. Blinding Flash of the Obvious Continuant Occurrent (Process, Event) Independent Continuant Dependent Continuant How to create an ontology from the top down 19

20. Example: The Cell Ontology

21. 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 21

22. 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 22

23. 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) 23

24. Users of BFO National Cancer Institute Biomedical Grid Terminology (BiomedGT) US Army Universal Core Semantic Layer (UCore SL) US Army Biometrics Ontology United Nations Environment Programme 24

25. 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 25

26. – 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 26

27. 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 27

28. Blinding Flash of the Obvious Continuant Occurrent (Process, Event) Independent Continuant Dependent Continuant How to create an ontology from the top down 28

29. 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 29 Red color of your skin depends_on

30. Continuant Independent Continuant Dependent Continuant.......... Non-realizable Dependent Continuant (quality) Realizable Dependent Continuant (function, role, disposition) 30

31. Realizable dependent continuants plan function role disposition capability tendency continuants 31

32. Their realizations execution expression exercise realization application course occurrents 32

33. Continuant Independent Continuant Dependent Continuant.......... Non-realizable Dependent Continuant (quality) Realizable Dependent Continuant (function, role, disposition) 33

34. realization depends_on realizable Continuant Occurrent Independent Continuant bearer Dependent Continuant disposition................ Process of realization 34

35. 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. 35

36. depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality................ temperature depends on bearer 36

37. 37 The (Aristotelian) Ontological Sextet SubstancesQuality entitiesProcesses Universals Substance- universals Quality- universals Process- universals Particulars Individual Substances Quality- instances (Tropes…) Process- instances

39. Specifically dependent continuants the quality of whiteness of this cheese your role as lecturer the disposition of this patient to experience diarrhea 39

40. 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 40

41. 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 41

42. depends_on Continuant Occurrent process Independent Continuant thing Dependent Continuant quality................ temperature depends on bearer 42

43. 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 43

44. 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 44

45. 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 45

46. Continuant Independent Continuant Specifically Dependent Continuant.......... Quality Realizable Dependent Continuant (function, role, disposition) 46

47. 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. 47

48. 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 48

49. Continuant Independent Continuant Specifically Dependent Continuant.......... Quality Realizable Dependent Continuant (function, role, disposition) 49

50. Realizable dependent continuants plan function role disposition capability tendency continuants 50

51. Their realizations execution expression exercise realization application course occurrents 51

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

53. 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

54. 54 http://bioportal.bioontology.org/ontologies/IAO

55. IAO-Intel IAO-Intel – an extension of IAO and incorporating features of the AIRS Information Ontology – to provide common resources for the consistent description of information artifacts of relevance to the intelligence community

56. IAO: Report / IAO-Intel: Intelligence Report IAO-Intel terms are defined by using terms from the ontologies in the yellow box via relations such as: is-about created-by derives-from and so forth

57. 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*) Extension Strategy + Modular Organization top level mid-level domain level Information Artifact Ontology (IAO) Ontology for Biomedical Investigations (OBI) Spatial Ontology (BSPO) Basic Formal Ontology (BFO) 57

58. Information Artifacts artifact =def. an entity created through some deliberate act or acts by one or more human beings and which endures through time information artifact: an artifact that can be the bearer of information (a) information artifact (IA) – a hard drive, a passport, a piece of paper with a drawing of a map (b) information content entity (ICE) – an entity which is about something and which can potentially exist in multiple (for example digital or printed) copies – a jpg file, a pdf file

59. Types and tokens Copyable information artifacts can exist both as tokens Peirce and as types Peirce Token = the particular information artifact of interest, tied to some particular physical information bearer: the photographic image on this piece of paper retrieved from this enemy combatant Type = The copyable information content that is carried by the artifact in question. The same photographic image type may be printed out in multiple paper tokens Warning: this is not the same as the instance-class distinction

60. IAO is designed to address the need for metadata standards, not by replacing existing standards, but rather by providing a single, consistent framework for tagging (‘semantic enhancement’) of existing data stores Its purpose is to provide a uniform, non- redundant, algorithmically processable and easily extendible consensus system of tags

61. Core of IAO TypeDefinitionIAO Information Content Entity (ICE) a generically dependent continuant that stands in the relation of aboutness to some entity ICE Information Structure Entity (ISE) a generically dependent continuant that is not an ICE but which is complemented or complementable by one or more ICEs to create another ICE (example: cell in a spreadsheet, hard line break, space between words, semi- colon) (new) Information Quality Entity (IQE) a quality that concretizes some ICE or ISE. (Comment: Typically an IQE will be a complex pattern made up of multiple qualities joined together spatially) Information Carrier Artifacta Material Entity that was created or modified or selected by some Agent to realize a certain function or to fulfill a certain role (Example: a screwdriver, a hard drive, a traffic sign) (new) Information Artifact (IA) an artifact whose function is to bear an IQE. (Examples: a hard drive, a blank sheet of paper, a passport, a currency note) (new) Planadded as primitive(new) 61

62. Attributes of IAs Information artifacts have attributes along a number of distinct dimensions, treated in low- level ontology modules Terms in these modules will be applied to explicate information relating to IAs of different sorts, and to annotate data pertaining to IA instances Attributes of IAs vs. Attributes of subject-matters, targets, topics, …

63. Attributes of IAs (cont.) Some dimensions of IA attributes are common to all areas, both military and non-military – Purpose – Life­cycle Stage (draft, finished version, revision) – Language, – Format – Provenance – Source (person, organization)

64. Generic Attributes of IAs (for IAO) Purpose – Descriptive purpose: scientific paper, newspaper article, after-action report – Prescriptive purpose: legal code, license, statement of rules of engagement – Directive purpose (of specifying a plan or method for achieving something): instruction, manual, protocol – Designative purpose: a registry of members of an organization, a phone book, a database linking proper names of persons with their social security numbers Purposes specific to IAO-Intel – Inform­ing the commander, – Providing targeting support – Intelligence preparation of the battlefield.

65. Descriptive purpose =def. the purpose of describing some portion of reality Examples: scientific paper, newspaper article, diary, experimenter log notebook Prescriptive purpose =def. the purpose of prescribing or permitting or allowing some activity Examples: a legal code, a license Purpose of an Information Artifact 65

66. Directive purpose =def. the purpose of specifying a plan or method for achieving something Examples: instruction, manual, recipe, protocol Designative purpose =def. the purpose of uniquely designating some entity or the members of some class of entities Examples: a registry of members of an organization, a phone book, a database linking proper names of persons with their social security numbers. Purpose of an Information Artifact 66

67. Examples of Generic Attributes of IAs Purpose Lifecycle Stage (draft, finished version, revision) Language Format Provenance Source (person, organization) These terms will be included in IAO Each corresponds to a specific low level ontology

68. Other IAO-Intel Attribute Dimensions Classification – Unclassified, open source – Secret – Top Secret Level – Strategic – Operational – Tactical Encryption Status Encryption Strength

69. Strategy for Building IAO-Intel Incremental expansion; the ontology is planned to include artifacts spanning the entire range of IAs, from authoritative data sources to unprocessed reports Identify orthogonal dimensions of IA attributes and create Low-Level Ontology modules (LLOs) – Small, shallow, and structured following the principle of single inheritance – Used to Construct more complex terms and define IAO terms Explicate the meanings of terms standardly used by different agencies Annotate instance data

70. IAO and BFO BFO: Generically Dependent Continuant BFO: Independent Continuant BFO: Specifically Dependent Continuant Information Content Entity (ICE) Information Quality Entity (Pattern) (IQE) Information Structure Entity (ISE) Information Artifact (IA)

71. Generically Dependent Continuant Generically Dependent Continuant pdf file jpg file 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 71

72. Information artifacts pdf file email poem symphony algorithm symbol – can migrate from one information artifact to another 72

73. Continuant Independent Continuant Specifically Dependent Continuant Quality Disposition Information Artifact Role Realizable Dependent Continuant 73 Generically Dependent Continuant Gene Sequence

74. Continuant Independent Continuant Specifically Dependent Continuant Quality Information Artifact 74 Generically Dependent Continuant Gene Sequence Material Entity Information Bearing Entity

75. Continuant Independent Continuant Specifically Dependent Continuant Quality Information Artifact 75 Generically Dependent Continuant Material Entity Information Bearing Entity (your hard drive Information Quality Entity (pattern on your hard drive) depends_on

76. Continuant Independent Continuant Specifically Dependent Continuant Quality Information Artifact 76 Generically Dependent Continuant Material Entity Information Bearing Entity Information Quality Entity depends_on concretized_by

77. IAO: information content entity =def. an entity that is generically dependent on some artifact and stands in the relation of aboutness to some entity 77

78. IAIBEISEICE MS Word file (.doc,.docx) Hard drive (magnetized sector) MS Word format Varies KML file Hard drive (magnetized sector) KML Map overlay JPEG file (.jpg) Hard drive (magnetized sector) JPEG format Image Email file Hard drive (magnetized sector) Internet Message Format (e.g., RFC 5322 compliant) Message USMTF Message file A specific government network USMTF Format Message Passport Paper document; (may include photographs, RFID tags) ID formats, security marking formats … Name, Personal data, Passport number, Visas Title DeedOfficial paper documentVaries ReportVaries Overlay Sheet ( e.g. Map Overlay Sheet) Acetate sheet MIL-STD-2525 Symbols; FM 101-1-5 Operational Terms and Graphics Map overlay

79. IAO and BFO BFO: Generically Dependent Continuant BFO: Independent Continuant BFO: Specifically Dependent Continuant Information Content Entity (ICE) Information Quality Entity (Pattern) (IQE) Information Structure Entity (ISE) Information Artifact (IA)

80. IAO and BFO (cont.) BFO relations between ICEs, ISEs, IQEs and IBEs can be set forth as follows: – ICE generically-depends-on IBE – ISE generically-depends-on IBE – IQE specifically-depends-on IBE – ICE concretized-by IQE – ISE concretized-by IQE IAO contains in addition relations which allow to formulate metadata concerning attributes of IAs such as author, creation date, classification status, and so forth