Social Event, Monday, November 18, 6pm

1. Social Event, Monday, November 18, 6pm

2. The Information Artifact Ontology:Roots in BFO Barry Smith October 14, 2013

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

4. Types and Instances Geographic Coordinates Set designates Geopolitical Entity Spatial Region instance_of has location is_a Village Name has location Distance Measurement Result designates Village Well Latrine instance_of instance_of instance_of instance_of instance_of ’16 meters’ ‘VT 334 569’ ‘Khanabad Village’ measurement_of located in located near

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

6. Specifically Dependent Continuants has unique bearer; if this bearer ceases to exist, then the quality or RDC ceases to exist the color of my skin the function of my heart John’s smile Specifically Dependent Continuant Quality, Pattern Realizable Dependent Continuant (RDC)

7. Generically Dependent Continuants Generically Dependent Continuant 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 Information Object Sequence

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

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

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

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

12. IAO: information content entity • =def. an entity that is generically dependent on some artifact and stands in the relation of aboutnessto 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?

13. 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)

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

16. The novel War and Peace has many bound copiesThe quality spherical has many instancesBut 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 Instances vs Copies

17. What is a work of literature? • 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.

18. There are not two Declarations of Independence • 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.

19. Rule for types • Theirnames are pluralizable • There canbethree people • There cannotbethree Michelle Obamas. • Information Content Entities are GDCs = entities which can exist in many copies

20. Generically dependent continuants are distinct from types • 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

21. 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

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

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

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

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

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

27. 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

28. Steps towards an email ontology • message has_partheader section and body section • header section has_parta collection of header fields • header 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

29. Steps towards an email ontology • 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 • …

30. E-mail Header

31. Email Address Field • 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

32. Purpose of an Information Artifact • 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

33. Purpose of an Information Artifact • 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.

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

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

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