1. The Information Artifact Ontology 1: Roots in BFO Barry Smith

3. Standardized information artifact metadata: 1. hardware 3

4. IAO Clinical

5. Continuant Occurrent Independent Continuant Dependent Continuant Quality Disposition Process Role Realizable Dependent Continuant 5

6. locate d near Latrin e Well ‘VT 334 569’ Distance Measurement Result Village Name ‘Khanabad Village’ Village is_a instance_ of Geopolitic al Entity Spatial Region Geographic Coordinate s Set designate s instance_of located in instance_ of has location designates has location instance_o f ’16 meters’ instance_of measurement_of 6 Types and Instances

7. Continuant Independent Continuant Specifically Dependent Continuant Quality Disposition Information Artifact Role Realizable Dependent Continuant 7 Generically Dependent Continuant Gene Sequence

8. Specifically Dependent Continuants Specifically Dependent Continuant Quality, Pattern Realizable Dependent Continuant if any bearer ceases to exist, then the quality or function ceases to exist the color of my skin the function of my heart 8

9. Generically Dependent Continuants Generically Dependent Continuant Information Object 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 9

10. Information artifacts pdf file email poem symphony algorithm symbol - can migrate from one information bearer to another 10

11. Continuant Independent Continuant Specifically Dependent Continuant Quality Information Artifact 11 Generically Dependent Continuant Gene Sequence Material Entity Information Bearing Entity

12. Continuant Independent Continuant Specifically Dependent Continuant Quality Information Artifact 12 Generically Dependent Continuant Material Entity Information Bearing Entity Information Quality Entity depends_on concretized_by

13. 13 http://bioportal.bioontology.org/ontologies/IAO

14. IAO: information content entity =def. an entity that is generically dependent on some artifact and stands in the relation of aboutness to some entity Problems Is a work of fiction about something? Is a fake cover story for a fake terrorist about something? Is an erroneous entry in a database about something? 14

15. Generically dependent continuants such as plans, laws … are concretized in specifically dependent continuants (the plan in your head, the protocol being realized by your research team, the law being implemented by this government agency) 15

16. War and Peace is an instance Specifically Dependent Continuant War and Peace quality 16 Independent Continuant This bound copy of War and Peace Generically Dependent Continuant The novel War and Peace instance_of depends_on concretized_by

17. 17

18. The novel War and Peace has many bound copies The quality spherical has many instances But having copies and having instances are two different things Information entities exist in a way which makes them dependent on provenance, and on processors, in a way in which types are not 18 Instances vs Copies

19. 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? 19

20. 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 Hence the US Declaration of Independent is an instance and not a type. There are not two Declarations of Independence 20

21. Rule for types Their names are pluralizable There can be three people There cannot be three Michelle Obamas. Information Content Entities are GDCs = entities which can exist in many copies 21

22. they have a different kind of provenance ◦ Aspirin as product of Bayer GmbH ◦ aspirin as molecular structure ◦ This Financial Report is submitted to the SEC Generically dependent continuants are distinct from types 22

23. Information content entity prior intent to be directed directedne ss rule- governed ness informs directedne ss for communicatio n denotation as part soldiernoyes noyes normal science yes doodleno fake message noyes noyes geez louiseyesno yesno googoogoono yesno

24. Your passport can be copied, but a copy of your passport cannot be your passport Boarding pass can be copied, and a copy of your boarding pass can be your boarding pass Passport vs. Boarding Pass 24

25. Terminology of types and tokens, vs. terminology of types and instances 25

26. Generically dependent continuants 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 – this is an information quality entity: a BFO:quality of the material (information bearing entity) that is the score 26

27. Generically dependent continuants (GDCs) can be concretized in multiple different media (paper, silicon, neuron …) 27

28. 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 28

29. Information Content Entity (science) protocol database theory ontology gene list publication result... 29

30. Information Content Entity (labeling) serial number batch number grant number person number name address email address URL... 30

31. Financial Report Financial Report in XBRL for submission to GAAP Business Report Information Content Entity (Finance) 31

32. Type or instance Continuant Occurrent (Process) Independent Continuant human being, protocol document Dependent Continuant pattern of ink marks Applying the protocol Side-Effect …................... 32

33. Continuant Occurrent Independent Continuant Dependent Continuant................ Information Content Entity Action creating a datum 33

34. do not require specific media (paper, silicon, neuron …) Generically dependent continuants 34

35. Generically Dependent Continuants Generically Dependent Continuant Information Content Entity Gene Sequence.pdf file.doc file instances 35

36. 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 36

37. 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 37

38. 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 38

39. Literary purpose =def. a Document whose primary purpose is to express products of imagination Purpose and kinds of aboutness 39

40. 40

41. Steps towards an email ontology message has_part header section and body section header section has_part a collection of header fields h eader field contains a header name and a header body header body may have additional structure based on the header in question body may have nested structure and attachments based on MIME the body may contain a text version, an HTML version, or both the body may contain attachments (files such as images, documents, other emails, etc header fields may use MIME to include header information in other languages/charsets

42. email may have_status draft, sent email may addressee may be in to: field, cc: field, bcc: field email may be forwarded email may be read, unread email may have priority label … Steps towards an email ontology 42

43. E-mail Header 43

44. A field is an information structure entity (comparable to cell, margin, space between words, period, comma, etc.) This means it is not about anything. Nearly all information content entities have fields as parts Address field is an information content entity which has a field as part But address field is about (in some very attenuated sense) the type: address Similarly the field in a spreadsheet where you fill in the measurement unit used is an ICE, because it is (in this same attenuated sense) the type: measurement unit. When you fill in the actual address then the resultant field is an ICE which is about that actual address BS Email Address Field 44

45. Information Artifact Ontology 2: Aboutness 45

46. 46 Shimon Edelman’s Riddle of Representation two humans, a monkey, and a robot are looking at a piece of cheese; what is common to the representational processes in their visual systems?

47. 47 Answer: The cheese, of course

48. 48 The real cheese

49. 49 the arrow of intentionality

50. ± simple mental processcontent(putative) target presenting act content of presentation “apple” object of presentation judging act judgment-content “the apple over there is ripe” state of affairs fact evaluating act emotional act appraisal … “it is good that the apple over there is ripe” ?

51. mental processcontenttarget you see an apple“apple”an apple you are in physical contact with target ―cf. Russell’s knowledge by acquaintance; J. J. Gibson’s ecological theory of perception ± relational intentionality

52. mental processcontent(putative) target presenting act sensory contentobject of presentation object exists object does not exist object present object absent ± perceptually filled ordinary perception

53. mental processcontent(putative) target presenting act sensory contentobject of presentation object exists object does not exist object present object absent perceptually filled does not imply veridical hallucination

54. perception involves also a further component you experience the object as causing your experience (cf. also pain …)

55. mental processcontent(putative) target presenting actcontent of presentation “apple” + sensation originating causally at target object of presentation object exists object does not exist object present object absent the evolutionarily most basic case ordinary perception

56. mental processcontent(putative) target presenting actcontent of presentation “apple” + sensation originating causally at target object of presentation object exists object does not exist object present object absent relational implies veridical ordinary perception

57. mental processcontent(putative) target presenting actcontent of presentation “apple” object of presentation object exists object does not exist object present object absent veridical does not imply relational veridical thinking about

58. mental processcontent(putative) target presenting actcontent of presentation “apple” object of presentation object exists object present object absent ± content match

59. content match “apple”

60. content match “food”

61. mental processcontent(putative) target presenting actcontent of presentation “apple” object of presentation object exists object present object absent veridical does not imply content match

62. content mismatch “poison”

63. content mismatch “apple” content here not just a matter of language still posson

64. mental processcontenttarget you see an apple“apple”an apple ± linguistically mediated A cat can see a king A cat can see a mass spectrometer

65. mental processcontentthere is no target presenting actcontent of presentation “apple” underlying false belief non-veridical intentionality is an untidy collection of non-canonical cases the presenting act is dependent on an underlying belief or attitude of one or other deviant types

66. mental processcontent(putative) target presenting actcontent of presentation “apple” object present object absent non-veridical intentionality type 1. ontological error hallucination, deception, … the presenting act is dependent on a false underlying belief

67. mental processcontent(putative) target presenting actcontent of presentation “apple” object present object absent non-veridical intentionality type 2. fiction thinking-about-Macbeth = the presenting act is not dependent on an underlying false belief “The Substitution Theory of Art”, Grazer Philosophische Studien, 25/26 (1986)

68. 68 the primacy of language (Sellars …) mental experiences are about objects because words have meaning word / meaning

69. 69 the primacy of the intentional (Brentano, Husserl, …): linguistic expressions have meanings because there are (‘animating’) mental experiences which have aboutness

70. dimension of content / belief prior to dimension of language

71. language comes later than mental aboutness 71

72. How annotate this 72

73. or this? 73

74. or this? 74

75. Mental Functioning Ontology (Draft)

76. with thanks to Janna Hastings and Kevin Mulligan Swiss Center for Affective Sciences)

77. Basic Formal Ontology 77 BFO:Entity BFO:Continuant BFO:Occurrent BFO:Process BFO:Independent Continuant BFO BFO:Dependent Continuant BFO:Disposition

78. Basic Formal Ontology and Mental Functioning Ontology (MFO) 78 BFO:Entity BFO:Continuant BFO:Occurrent BFO:Process Organism BFO:Independent Continuant BFO MFO BFO:Dependent Continuant Behaviour inducing state Mental Functioning Related Anatomical Structure Cognitive Representation BFO:Quality Affective Representation Mental Process Bodily Process BFO:Disposition

79. Functions vs. Functionings Continuants vs. Occurrents 79 BFO:Entity BFO:Continuant BFO:Occurrent BFO:Process Organism BFO:Independent Continuant BFO MFO BFO:Dependent Continuant Mental Function Cognitive Representation BFO:Quality Mental Process Bodily Process BFO:Disposition Mental Functioning

80. Aboutness (‘Intentionality’) 80 BFO:Entity BFO:Continuant BFO:Occurrent BFO:Process Organism BFO:Independent Continuant BFO MFO BFO:Dependent Continuant Mental Function Cognitive Representation BFO:Quality Mental Process Bodily Process BFO:Disposition Mental Functioning does all mental functioning involve cognitive representation (aboutness)? what is aboutness?

81. Extending the MFO to linguistic competence and performance 81

82. Linguistic Functioning Ontology (1. Speech and hearing) 82 BFO:Entity BFO:Continuant BFO:Occurrent BFO:Process BFO:Independent Continuant BFO MFO BFO:Dependent Continuant Behaviour inducing state Cognitive Representation BFO:Quality Speech- mediated cognitive representation Speech process Bodily Process BFO:Disposition Linguistic competence Speech competence of a population = a [spoken] language Speech competence of an individual Hearing (registering) process

83. Linguistic Functioning Ontology (2. Reading and writing) 83 BFO:Entity BFO:Continuant BFO:Occurrent BFO:Process BFO:Independent Continuant BFO MFO BFO:Dependent Continuant Behaviour inducing state Cognitive Representation BFO:Quality Written- language- mediated cognitive representation Writing process Bodily Process BFO:Disposition Linguistic competence Written linguistic competence of a population = a [written] language Written linguistic competence of an individual Reading (registering) process

84. Linguistic Functioning Ontology (the whole thing) 84 BFO:Entity BFO:Continuant BFO:Occurrent BFO:Process BFO:Independent Continuant BFO MFO BFO:Dependent Continuant Behaviour inducing state Cognitive Representation BFO:Quality Language- mediated cognitive representation Writing Bodily Process BFO:Disposition Linguistic competence Linguistic competence of a population = a language Linguistic competence of an individual Reading Speaking

85. mental processcontent(putative) target presenting actcontent of presentation “apple” object present object absent non-veridical intentionality type 3. planning Christmas present lists

86. mental processcontent(putative) target presenting actcontent of presentation “apple” object present object absent non-veridical intentionality type 4. daydreaming

87. Geach’s witch Hob thinks a witch has blighted Bob’s mare, and nob wonders whether she (the same witch) killed Cob's sow. Cf. fake terrorists

88. Mental Functioning Ontology (MF) 88 brain in endocrine gland

89. Aboutness 89 brainretina ENVIRONMENT

90. mental act about a real-world object non-relational (~ linguistic) relational (~ perception) content match content mismatch content match content mismatch veridical non-veridical 90

91. mental processcontent(putative) target presenting actcontent of presentation “apple” object of presentation object exists object does not exist target present target absent Veridical intentionality ordinary perception evolutionarily most basic case 91

92. 92

93. 93 BFO:Entity BFO:Continuant BFO:Occurrent BFO:Process BFO:Independent Continuant BFO MFO BFO:Dependent Continuant Behaviour inducing state Cognitive Representation BFO:Quality Language- mediated cognitive representation Writing Bodily Process BFO:Disposition Linguistic competence Linguistic competence of a population = a language Linguistic competence of an individual Reading Speaking what is a language? something analogous to a biological species (a population of competences)

94. The Information Artifact Ontology 3: Dublin Core Barry Smith

95. The problem Keeping track of data; finding data Information artefacts = carriers of data/information, for example reports Data have metadata – date created, author … To solve the problem of keeping track of data we need to address – 1. what are the data about  data topics – 2. how the data are packaged (collected, presented, formatted, stored)  resources, information artifacts

96. RDF = Resource Description Framework What is a ‘resource’?

98. Dublin Core Elements & Uses 15 metadata elements 15 metadata elements for the description of resources… especially digital resources. http://dublincore.org/ Jody DeRidder, Digital Libraries IS 565, Spring 2007

99. 1) What’s a “resource”?resource  A resource is anything that has identity. Familiar examples include an electronic document, an image, a service (e.g., "today's weather report for Los Angeles"), and a collection of other resources. 2) How do “elements” apply to “resources”?elements  An Element is a characteristic that a resource may “have”, such as a Title, Publisher, or Subject. 3) What if I have more than one version of this resource?

100. The same resource can be instantiated in different ways LanguageLanguage: A language of the resource. Recommended best practice is to use a controlled vocabulary such as ISO 639-2. Example: “eng” for English.ISO 639-2 DateDate: A date associated with the creation or availability of the resource. Recommended best practice is defined in a profile of ISO 8601 that includes (among others) dates of the forms YYYY and YYYY-MM-DD.ISO 8601 FormatFormat: The file format, physical medium, or dimensions of the resource. Examples of dimensions include size and duration. Recommended best practice is to use a controlled vocabulary such as the list of Internet Media Types [MIME]. Example: image/jpeg.MIME

101. http://www.referent- tracking.com/RTU/?page=ceusters_vita

102. http://www.referent- tracking.com/RTU/?page=ceusters_vita

104. 2 seconds later

105. what describes the content / topic / subject- matter? TitleTitle: The name given to the resource. DescriptionDescription: An account of the content of the resource. Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. SubjectSubject: The topic of the content of the resource. Typically, a subject will be expressed as keywords or key phrases or classification codes that describe the topic of the resource. SourceSource: A reference to a resource from which the present resource is derived. The present resource may be derived from the Source resource in whole or part. TypeType: The nature or genre of the content of the resource. Type includes terms describing general categories, functions, genres, or aggregation levels for content.

106. what describes who made it? CreatorCreator: An entity primarily responsible for making the content of the resource. Examples of a Creator include a person, an organization, or a service. ContributorContributor: An entity responsible for making contributions to the content of the resource. Examples of a Contributor include a person, an organization or a service. Typically, the name of a Contributor should be used to indicate the entity. PublisherPublisher: The entity responsible for making the resource available. Examples of a Publisher include a person, an organization, or a service. Typically, the name of a Publisher should be used to indicate the entity.

107. All 15 elements of Simple Dublin Core Instantiation: Date Format Identifier Language Content: Title Description Coverage Relation Source Subject Type Intellectual Property: Contributor Creator Publisher Rights

108. Type of Qualifier ElementExample Qualifiers Element Refinement DescriptionAbstractAbstract, tableOfContentstableOfContents CoverageSpatialSpatial, TemporalTemporal DateAvailableAvailable, Created, dateCopyrighted, dateAccepted, dateSubmittedCreateddateCopyrighteddateAccepted dateSubmitted RelationhasParthasPart, hasVersion, isPartOf, isReferencedBy, isReplacedby, isVersionOfhasVersionisPartOfisReferencedBy isReplacedbyisVersionOf Encoding Schemes SubjectDDCDDC (Dewey Decimal Classification), LCCLCC (Library of Congress Classification), LCSHLCSH (Library of Congress Subject Headings), MESHMESH (Medical Subject Headings)… LanguageISO639-2 ISO639-2 (such as eng, for English), RFC1766 (such as en-us for US English)RFC1766 Date W3CDTFW3CDTF (such as 1997-12-04 for 4 Dec. 1997) TypeDCMITypeDCMIType, such as: Collection, Dataset, Event, Image, InteractiveResource, MovingImage, PhysicalObject, Service, Software, Sound, StillImage, Text. Some example qualifiers…

109. Example online represenatation

111. http://dublincore.org/documents/2012/06/14 /dcmi-terms/#terms-abstract http://dublincore.org/documents/2012/06/14 /dcmi-terms/#terms-abstract Dublin Core (~ OWL) BFO PropertiesRelations Terms ClassesTypes Instances

112. located near from Bill Mandrick 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 112

115. Dublin Core CREATED is a property in Dublin Core Properties (relations) have a domain and a range Why is the Range of this property not entities with the DATE data type?