1. New York State Center of Excellence in Bioinformatics & Life Sciences R T U I 3 : Identity, Identifiers, Identification Referent Tracking and its Applications WWW2007 – Banff, May 8th, 2007 Werner CEUSTERS Center of Excellence in Bioinformatics and Life Sciences Ontology Research Group University at Buffalo, NY, USA

2. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Imagine being in Saudi-Arabia, ready to open this window …

3. New York State Center of Excellence in Bioinformatics & Life Sciences R T U These are ‘First Order Entities’ This specific guy (#1) This specific ‘silver’ Audi (#2) This specific brick (#3)

4. New York State Center of Excellence in Bioinformatics & Life Sciences R T U But we are not here …

5. New York State Center of Excellence in Bioinformatics & Life Sciences R T U We are in something close to this … This specific image of #1 (#4) This specific image of #2 (#5) This specific image of #3 (#6) These are first order objects too …

6. New York State Center of Excellence in Bioinformatics & Life Sciences R T U … as well as second order #4 stands-for? #1 #6 stands-for? #3

7. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Not just first order is “in reality”, But so is second order

8. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Second order “in” first order An image of #9 (the hotel from which we would be looking to this car) (#10)

9. New York State Center of Excellence in Bioinformatics & Life Sciences R T U A different look on #8 as first order entity (What would be #7 ?) ÿØÿà JFIF H H ÿáGExif MM * b j( 1 % r2 —‡i ¬ Ø ü€ ' ü€ 'Adobe Photoshop Elements 4.0 Windows 2007:01:05 10:15:48 ~ ² &.( 6 H H ÿØÿà JFIF H H ÿí Adobe_CM ÿî Adobe d€ ÿÛ „ ÿÀ " ÿÝ ÿÄ? 3 !1AQa"q2‘¡±B#$RÁb34r‚ÑC%’Sðáñcs5¢²ƒ&D“TdE£t6ÒUâeò³„ÃÓuãóF'”¤…´ÄÔäô¥µÅÕåõVfv†– ¦¶ÆÖæö7GWgw‡—§·Ç×ç÷ 5 !1AQaq"2‘¡±B#ÁRÑð3$bár‚’CScs4ñ%¢²ƒ&5ÂÒD“T£dEU6teâò³„ÃÓuãóF”¤…´ÄÔäô¥µÅÕåõVfv†– ¦¶ÆÖæö'7GWgw‡—§·ÇÿÚ ? àñ~´uüHf?hü×ÃÇþ·°?ÆâÔ(k΀¾±´ýÁqz¤e3„tÓÉšûêúŽ'×.ƒ“ Üiw…ƒOón¿Õ[™Spú]­ ¹ÖÉ±ì †³‚çþêóL $ ®Ç¾ÓCý*àîãOm?õ¿ú´MjtüU`ÊÅß©c¼UŒÍö¸öh'Ý·óÞç{L:mC)Ù̵µµÀÖààD·k\ßÞÙ*m¯5´dê43'[r_ô™SZMµ3éú Ü©U‘‹fV+)¡´ÑE’,?μ»ŽM¿žßÑþŽ¿ð[ސÓUÙÁû[3îÏû3žË…Ž±Â–-skìÛú?Ké¡u©†z5;Ø­õ¬º²ýÎsÜݶ2¦îö~…¿£ö+y}O ùÆÛ^ö¶ZáHÈsH—mg¬æÐÍŸ¿·zÍÆ»%ÙTcÛ“Sڍ°Øylxc_ù¾ö{“´Z’ΉœCow¥Cío©U í0<#w¦ÿ oÐzc×3ŸW¡µ­ ÉqÚìE³1ý‡ªÇ«uc¬8n3·–ghk¿56Nmyאj´mˆÚòíÁ±íA.Å™Ub´dõ;um5=ð o>æ{mnê¿7ÿ °Í»ísöµÆCX!£É¡m³­ ôÇeÔ,eŸe1¿cnÜÒvºÖmc¾Ÿówìþmeu&ìÍxô[@0vVà澧·Û±étPzªeõ\0.tãÛ>™ì×ÿ 枺ò5^[sëp,vÓÙzAêmê]9– 7ÔwŽû€ÒÏúïÒMî’:·ˆQ!¨V°**eGºIÿÐóVCw [ÁŽß'²W>·nøƒÁY'PXécāÿ })º²éVèýXÆõ´<K1Fñ?¾}µÿ ›ôÕþ·–O´%Úžú+;ôî– ðu¿¥¼ñ={ú6¬ž xuÔþ’¦}'¶{øiîjlEDjÔ9¹§ã‡ŸNÒ7—jtÎwõSpæ~ŽêœGæZ³êµŒwùè!°}þß tü©:O}K!‹q ;kgwÓpGénŸ¡ýµkí™mÇ­®s+¢ùƒË†Ïn÷1®ß¿÷78¨1®±Á¬îw h’~MNRV×K½ößeâ œg÷?5ßÛs¶êÌ·¯J³§¸ïy˲ý±jôï©ýk6êÆ-f!÷’Òg÷knçÿ œºÞ›õ3£bÒEc.É!Ö] <²©ÚÖ¦JqŽåtqÊ[µáz_EÎêŽÙšu ²×˜c“ü§ÿ !iÛõ/ªVÀYm/ÒCIsOâ6¯A¯ŠêãÒÚ1Ù¨cö=ÀÝFsÐhÊ0Ôëàù{¾¯õªÌWÛšZá÷‡+ý+3£æ›m©Â‡K(hà ?IÛ ¶:½Û×hüa¶@ç·ÅbgâØë‡q¶ØîÑô_ýz’÷/¢*êôR×

10. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Close your eyes … Try to imagine that specific ‘silver’ car … If everybody succeeded, there is #11, #12, #13, … i.e. a ‘mental image’ inside each of the attendees in this room

11. New York State Center of Excellence in Bioinformatics & Life Sciences R T U A wealth of distinct, though closely related things The guy (of flesh and blood) standing next to that ‘silver’ car The images of that guy embodied in the projections on the screen a bit earlier The bits in the PP-file on this laptop that cause PP and the OS on this laptop and … to project an image of that guy on the screen The mental images of that guy in each of you, as well as the mental images of the images of that guy …

12. New York State Center of Excellence in Bioinformatics & Life Sciences R T U The essence of Referent Tracking Keeping track of entities in reality By means of singular and globally unique identifiers (#1, #2, #3, …) That function as surrogates for these enities in information systems, documents, etc Ceusters W. and Smith B. Tracking Referents in Electronic Health Records. In: Engelbrecht R. et al. (eds.) Medical Informatics Europe, IOS Press, Amsterdam, 2005;:71-76

13. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Thus: when WE use “#12” WE refer to THIS

14. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Unfortunately, it is not that easy … What is ‘THIS’ … –The car ? –The door ? –The reflected image of the hotel ? –That pixel on this image ? –… #12

15. New York State Center of Excellence in Bioinformatics & Life Sciences R T U What is really needed … A ‘formal’ mechanism to –Assign numbers to entities –Specify :what the entities are –how they are related –Keep inventories of numbered entities –Let ‘systems’ know what number is assigned to an entity, and what entity is denoted by an assigned number

16. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Does mainstream SW thinking acknowledges this ? The answer is clearly: NO ! –Overemphasis on syntactic regimentation XML, RDF(s), OWL, … each have a semantics but users tend to assign more semantics to expressions therein than is actually carried. –Unwarranted trust in the power of description logics –Expressions in SW languages or ontologies are said to refer to ‘concepts’ –A complete mess in the terminology adhered to: Instance, object, resource, class, …

17. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Our proposal A combination of three theories/paradigms/... 1.Basic Formal Ontology what entities exist and how they are related 2.Granular Partition Theory how representations relate to reality 3.Referent Tracking how particular entities can be described unambiguously

18. New York State Center of Excellence in Bioinformatics & Life Sciences R T U BFO & GPT: a realist view of the world 1.The world exists ‘as it is’ prior to a cognitive agent’s perception thereof; 2.Cognitive agents build up through observations cognitive representations of the world; 3.To make these representations publicly accessible in some enduring fashion, these agents create representational artifacts that are fixed in some medium. Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

19. New York State Center of Excellence in Bioinformatics & Life Sciences R T U A realist view of the world The world consists of –entities that are Either particulars or universals; Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

20. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Particulars versus Universals

21. New York State Center of Excellence in Bioinformatics & Life Sciences R T U A realist view of the world The world consists of –entities that are Either particulars or universals; Either occurrents or continuants; Either dependent or independent; and, –relationships between these entities of the form e.g. is-instance-of, e.g. is-member-of e.g. isa (is-subtype-of) Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

22. New York State Center of Excellence in Bioinformatics & Life Sciences R T U A widespread misconception ‘A variety of clinical terminology standards exist in the health care system, giving meaning to raw data and allowing for semantic interoperability. Systemized Nomenclature of Medicine (SNOMED) clinical terms are one example of a clinical reference terminology that provides for semantic interoperability.’ Pharmacotherapy. 2005;25(8):1116-1125.

23. New York State Center of Excellence in Bioinformatics & Life Sciences R T U 557204/07/199026442006closed fracture of shaft of femur 557204/07/199081134009Fracture, closed, spiral 557212/07/199026442006closed fracture of shaft of femur 557212/07/19909001224Accident in public building (supermarket) 557204/07/199079001Essential hypertension 093924/12/1991255174002benign polyp of biliary tract 230921/03/199226442006closed fracture of shaft of femur 230921/03/19929001224Accident in public building (supermarket) 4780403/04/199358298795Other lesion on other specified region 557217/05/199379001Essential hypertension 29822/08/19932909872Closed fracture of radial head 29822/08/19939001224Accident in public building (supermarket) 557201/04/199726442006closed fracture of shaft of femur 557201/04/199779001Essential hypertension PtIDDateObsCodeNarrative 093920/12/1998255087006malignant polyp of biliary tract Three references of hypertension for the same patient denote three times the same disease. If two different fracture codes are used in relation to observations made on the same day for the same patient, they might refer to the same fracture The same type of location code used in relation to three different events might or might not refer to the same location. If the same fracture code is used for the same patient on different dates, then these codes might or might not refer to the same fracture. The same fracture code used in relation to two different patients can not refer to the same fracure. If two different tumor codes are used in relation to observations made on different dates for the same patient, they may still refer to the same tumor. Using codes does not prevent ambiguities as to what is described: how many disorders are listed?

24. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Consequences Very difficult to: –Count the number of (numerically) different diseases Bad statistics on incidence, prevalence,... Bad basis for health cost containment –Relate (numerically the same or different) causal factors to disorders: –Dangerous public places (specific work floors, swimming pools), –dogs with rabies, –HIV contaminated blood from donors, –food from unhygienic source,... Hampers prevention –...

25. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Purpose: –explicit reference to the concrete individual entities relevant to the accurate description of each patient’s condition, therapies, outcomes,... Proposed Solution: Referent Tracking Now! That should clear up a few things around here ! Ceusters W, Smith B. Strategies for Referent Tracking in Electronic Health Records. J Biomed Inform. 2006 Jun;39(3):362-78.

26. New York State Center of Excellence in Bioinformatics & Life Sciences R T U 78 Numbers instead of words Method: –Introduce an Instance Unique Identifier (IUI) for each relevant particular (individual) entity

27. New York State Center of Excellence in Bioinformatics & Life Sciences R T U ‘John Doe’s ‘John Smith’s liver tumor was treated with RPCI’s irradiation device’ ‘John Doe’s liver tumor was treated with RPCI’s irradiation device’ The principle of Referent Tracking #1 #3 #2 #4 #5 #6 treating person liver tumor clinic device instance-of at t 1 #10 #30 #20 #40 #5 #6 inst-of at t 2 inst-of at t 2 inst-of at t 2 inst-of at t 2 inst-of at t 2

28. New York State Center of Excellence in Bioinformatics & Life Sciences R T U EHR – Ontology “collaboration”

29. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Advantage: better reality representation 557204/07/199026442006closed fracture of shaft of femur 557204/07/199081134009Fracture, closed, spiral 557212/07/199026442006closed fracture of shaft of femur 557212/07/19909001224Accident in public building (supermarket) 557204/07/199079001Essential hypertension 093924/12/1991255174002benign polyp of biliary tract 230921/03/199226442006closed fracture of shaft of femur 230921/03/19929001224Accident in public building (supermarket) 4780403/04/199358298795Other lesion on other specified region 557217/05/199379001Essential hypertension 29822/08/19932909872Closed fracture of radial head 29822/08/19939001224Accident in public building (supermarket) 557201/04/199726442006closed fracture of shaft of femur 557201/04/199779001Essential hypertension PtIDDateObsCodeNarrative 093920/12/1998255087006malignant polyp of biliary tract IUI-001 IUI-003 IUI-004 IUI-005 IUI-007 IUI-002 IUI-012 IUI-006 7 distinct disorders

30. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Essentials of Referent Tracking Generation of universally unique identifiers; deciding what particulars should receive a IUI; finding out whether or not a particular has already been assigned a IUI (each particular should receive maximally one IUI); using IUIs in the EHR, i.e. issues concerning the syntax and semantics of statements containing IUIs; determining the truth values of statements in which IUIs are used; correcting errors in the assignment of IUIs.

31. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Architecture of a Referent Tracking System (RTS) RTS: system in which all statements referring to particulars contain the IUIs for those particulars judged to be relevant. Ideally set up as broad as possible: – some metrics: % of particulars referred to by means of IUI % of HCs active in a region –Geographic region –functional region: defined by contacts amongst patients % of patients referred to within a region Services: –IUI generator –IUI repository: statements about assignments and reservations –Referent Tracking ‘Database’ (RTDB): index (LSID) to statements relating instances to instances and classes

32. New York State Center of Excellence in Bioinformatics & Life Sciences R T U IUI assignment = an act carried out by the first ‘cognitive agent’ feeling the need to acknowledge the existence of a particular it has information about by labelling it with a UUID. ‘cognitive agent’: –A person; –An organisation; –A device or software agent, e.g. Bank note printer, Image analysis software.

33. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Criteria for IUI assignment (1) 1.The particular’s existence must be determined: –Easy for persons in front of you, body parts,... –Easy for ‘planned acts’: they do not exist before the plan is executed ! Only the plan exists and possibly the statements made about the future execution of the plan –More difficult: subjective symptoms But the statements the patient makes about them do exist ! –However: no need to know what the particular exactly is, i.e. which universal it instantiates No need to be able to point to it precisely –One bee out of a particular swarm that stung the patient, one pain out of a series of pain attacks that made the patient worried –But: this is not a matter of choice, not ‘any’ out of...

34. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Criteria for IUI assignment (2) 2.The particular’s existence ‘may not already have been determined as the existence of something else’: Morning star and evening star Himalaya Multiple sclerosis 3.May not have already been assigned a IUI. 4.It must be relevant to do so: Personal decision, (scientific) community guideline,... Possibilities offered by the EHR system If a IUI has been assigned by somebody, everybody else making statements about the particular should use it

35. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Assertion of assignments IUI assignment is an act of which the execution has to be asserted in the IUI-repository: –D i = IUI d IUI of the registering agent A i the assertion of the assignment »IUI a IUI of the author of the assertion »IUI p IUI of the particular »t ap time of the assignment t d time of registering A i in the IUI-repository Neither t d or t ap give any information about when # IUI p started to exist ! That might be asserted in statements providing information about # IUI p.

36. New York State Center of Excellence in Bioinformatics & Life Sciences R T U PtoP statements - particular to particular ordered sextuples of the form R i = IUI a is the IUI of the author of the statement, t a a reference to the time when the statement is made, r a reference to a relationship (available in o) obtaining between the particulars referred to in P, o a reference to the ontology from which r is taken, P an ordered list of IUIs referring to the particulars between which r obtains, and, t r a reference to the time at which the relationship obtains. P contains as much IUIs as required by the arity of r. In most cases, P will be an ordered pair such that r obtains between the particular represented by the first IUI and the one referred to by the second IUI. As with A statements, these statements must also be accompanied by a meta-statement capturing when the sextuple became available to the referent tracking system.

37. New York State Center of Excellence in Bioinformatics & Life Sciences R T U PtoU statements – particular to universal U i = IUI a is the IUI of the author of the statement, t a a reference to the time when the statement is made, inst a reference to an instance relationship available in o obtaining between p and cl, o a reference to the ontology from which inst and u are taken, IUI p the IUI referring to the particular whose inst relationship with u is asserted, u the universal in o to which p enjoys the inst relationship, and, t r a reference to the time at which the relationship obtains.

38. New York State Center of Excellence in Bioinformatics & Life Sciences R T U PtoN-statements N i = The person referred to by IUI a asserts at time t a that n i is the name of the nametype nt j that designates in the real world the particular referred to by IUI p at t r. This template will further be referred to as PtoN template. Would assert that “Werner” is my first name, and “Ceusters” is my last name.

39. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Ultimate goal #IUI-1 ‘affects’ #IUI-2 #IUI-3 ‘affects’ #IUI-2 #IUI-1 ‘causes’ #IUI-3... Referent Tracking Database EHR CAG repeat Juvenile HD person disorder continuant Ontology

40. New York State Center of Excellence in Bioinformatics & Life Sciences R T U RT for Digital Rights Management

41. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Conclusion The Semantic Web