1. Werner Ceusters & Shahid Manzoor
InterOntology Applying Referent Tracking to the Use and Evolution of Websites. Keio University, Tokyo, Japan - February 28, 2009
Werner Ceusters & Shahid Manzoor
Ontology Research Group
Center of Excellence in Bioinformatics & Life Sciences
SUNY at Buffalo, NY

2. Presentation overview
Foundations of referent tracking
Referent Tracking Systems
Referent Tracking enabled websites

3. Foundations of Referent Tracking

4. In (computational) linguistics:
‘Referent Tracking’
In (computational) linguistics:
Identifying which words or phrases denote the same entity throughout a discourse.
In the newspaper:
Obama gave another speech yesterday. The President said hard times are coming. But he was confident to come up with solutions.

5. In (computational) linguistics:
‘Referent Tracking’
In (computational) linguistics:
Identifying which words or phrases denote the same entity throughout a discourse.
In the newspaper:
Obama gave another speech yesterday. The President said hard times are coming. But he was confident to come up with solutions.

6. Origin: the semantic / semiotic triangle
concept
object
term
referent
reference

7. How can we know what co-refers?
prior mention
mutual knowledge from shared experience
frames/scripts/schemata: culturally established scenes with certain expectable parts
the handlebars from a mention of a bicycle;
the waiter from a mention of a restaurant
uniqueness in the “universe of discourse” (e.g. ‘the sun’)

8. Important local negotiation aspect during human communication
Not fail proof
Important local negotiation aspect during human communication
Requests for comprehension
‘you know ?’, ‘you remember ?’
Requests for clarification
‘who do you mean?’
Explanations
These tools are not available in isolated descriptions

9. Yolk or white in which case ?
From two recipes
For meringue:
Take an egg, separate the yolk from the white, add sugar and start beating it gently
For sabayon:
Take an egg, separate the yolk from the white, add sugar and white wine and start beating it gently over a low flame
Yolk or white in which case ?

10. A medical example: morbidity reporting
5572
04/07/1990
closed fracture of shaft of femur
Fracture, closed, spiral
12/07/1990
Accident in public building (supermarket)
79001
Essential hypertension
0939
24/12/1991
benign polyp of biliary tract
2309
21/03/1992
47804
03/04/1993
Other lesion on other specified region
17/05/1993
298
22/08/1993
Closed fracture of radial head
01/04/1997
PtID
Date
ObsCode
Narrative
20/12/1998
malignant polyp of biliary tract

11. The problem
Generic terms used to denote specific entities do not have enough referential capacity
Usually enough to convey that some specific entity is denoted,
Not enough to be clear about which one in particular.
For many ‘important’ entities, unique identifiers are used:
UPS parcels
Patients in hospitals
VINs on cars …

12. Fundamental goals of ‘our’ Referent Tracking
explicit reference to the concrete individual entities relevant to the accurate description of some portion of reality, ...
Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health Records. J Biomed Inform Jun;39(3):

13. Method: numbers instead of words
Introduce an Instance Unique Identifier (IUI) for each relevant particular (individual) entity
235 78
5678
321
322
666
427
Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health Records. J Biomed Inform Jun;39(3):

14. Fundamental goals of ‘our’ Referent Tracking
Use these identifiers in expressions using a language that acknowledges the structure of reality
e.g.: a yellow ball:
#1: the ball #2: #1’s yellow
Then not:
ball(#1) and yellow(#2) and hascolor(#1, #2)
But:
instance-of(#1, ball, since t)
instance-of(#2, yellow, since t)
inheres-in(#1, #2, since t)
Strong foundations
in realism-based
ontology

15. Codes for types AND identifiers for instances
5572
04/07/1990
closed fracture of shaft of femur
Fracture, closed, spiral
12/07/1990
Accident in public building (supermarket)
79001
Essential hypertension
0939
24/12/1991
benign polyp of biliary tract
2309
21/03/1992
47804
03/04/1993
Other lesion on other specified region
17/05/1993
298
22/08/1993
Closed fracture of radial head
01/04/1997
PtID
Date
ObsCode
Narrative
20/12/1998
malignant polyp of biliary tract
IUI-001
IUI-003
IUI-004
IUI-005
IUI-007
IUI-002
IUI-012
IUI-006

16. The semantic triangle revisited
Representation and Reference
First Order Reality
concepts
about
terms
concepts
objects
terms

17. Terminology Realist Ontology
Representation and Reference
concepts
terms
representational units
universals
particulars
about
objects
First Order Reality

18. Terminology Realist Ontology
Representation and Reference
concepts
terms
representational units
about
objects
universals
particulars
First Order Reality

19. Terminology Realist Ontology
Representation and Reference
representational units
concepts
terms
cognitive
units
communicative
units
about
objects
universals
particulars
First Order Reality

20. Three levels of reality in Realist Ontology
Representation and Reference
Representational units in various
forms about (1), (2) or (3)
representational units
cognitive
units
communicative
units
(2) Cognitive entities which are our
beliefs about (1)
(1) Entities with objective existence
which are not about anything
universals
particulars
First Order Reality

21. Representation and the three levels
Level 1, 2 or 3
Level 2 or 3
Level 3
Level 1

22. Possible mismatches reality / representations

23. Referent Tracking Systems

24. Referent Tracking System Environment

25. RTS farms … RTS Proxy Peer RTS Server Proxy
Referent Tracking Server C2
Referent Tracking Server C3 …
Referent Tracking Server B2
Referent Tracking Server B3
Referent Tracking Server A2
Referent Tracking Server A3
Information System A
Information System C
Information System B
Referent Tracking Server B1
Referent Tracking Server C1
Referent Tracking System C
Referent Tracking Server A1
Referent Tracking System A
Referent Tracking System B

26. Referent Tracking enabled Websites

28. Architecture

29. Some central ideas
Informative websites are about portions of reality. If the latter change, so should the former.
Synchronization should be auditable.
Enforce responsibility of information providers and consumers, yet protect their integrity.
Cross-fertilization with Information Artifact Ontology.

30. Some key insights Static versus dynamic pages;
Web pages usually keep their name (URL), yet undergo changes;
‘page’ versus ‘file’
Server file never ‘changes’: always replaced by a new file with the same name
Changes to a file do not always involve changes to the propositional content;
Requests to view a page do not lead the file on the server to be transmitted, but a new copy of it in each single case;

31. Entities to assign IUIs to
The content file of each page
The content of each content file
The propositional content of each content
Each browser page
Each checksum
Each ontology and terminology used in RT-tuples
Each RT-tuple (except D-tuples)
The middleware component

32. Use of the CEN Time Standard for HIT

33. Tuple generations when adding a page

34. Tuple generations when updating a page

35. Tuple insertions: generating a browser page
A-tuples n
IUIp
IUIa
tap
Key 1
#24 #2
(EVENT("#24 assignment") has-occ AT TP(time-18))
#25 3
#27
(EVENT("#27 assignment") has-occ AT TP(time-20))
#28 9
#34
(EVENT("#34 assignment") has-occ AT TP(time-26))
#35
D-tuples n
IUId
IUIA td E C S
Key 2 #2
#25
(EVENT("#25 inserted") has-occ AT TP(time-19)) I CE
#26 4
#28
(EVENT("#28 inserted") has-occ AT TP(time-21))
#29 6
#30
(EVENT("#30 inserted") has-occ AT TP(time-23))
#31 8
#32
(EVENT("#32 inserted") has-occ AT TP(time-25))
#33 10
#35
(EVENT("#35 inserted") has-occ AT TP(time-27))
#36 12
#37
(EVENT("#37 inserted") has-occ AT TP(time-29))
#38
PtoP-tuples n
IUIa ta r
IUIo P tr
Key 5 #2
(EVENT("#30 is asserted") has-occ AT TP(time-22))
MainContentCopyOf
#022
#27, #12
(EPISODE("#30 is true") has-occ SINCE TI(time-20))
#30 7
(EVENT("#32 is asserted") has-occ AT TP(time-24))
InstigatorOf
#24, #27
(EVENT ("#32 is true") has-occ AT TP(time-18))
#32 11
(EVENT("#37 is asserted") has-occ AT TP(time-28))
ChecksumOf
#34, #27
(EPISODE("#37 is true") has-occ SINCE TI(time-26))
#37

36. You see this is ontology! I got a graph!

40. Challenges for the Information Artifact Ontology
Ontological basis for various relationships that are currently too much CS-ish
MainContentCopyOf
InstigatorOf
DerivesFrom (applicable in this context?) …
Ontological nature of files, pages, content, propositional content

41. Future work
Better automatisation
Integration in popular web-design softwares
RT-enabled vita-publisher
Expansion to hard-copies