1. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Discovery Seminar 118330/UE 141 CC – Fall 2007 Difficult Problems, Easy Solutions: Referent Tracking in Biomedicine Session 1: 08/27/2007 Introduction: understanding the problem 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 Short personal history 1959 - 2006 1977 1989 1992 1998 2002 2004

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

4. 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)

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

6. 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 … So what do we really see ?

7. 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

8. 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

9. 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)

10. New York State Center of Excellence in Bioinformatics & Life Sciences R T U A different look on #8 as first order entity 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×

11. 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

12. 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 …

13. New York State Center of Excellence in Bioinformatics & Life Sciences R T U What is the problem ? These entities, specifically their status as being first or second order entities, get mixed up. A message to map makers: “Highways are not painted red, rivers don’t have county lines running down the middle, and you can’t see contour lines on a mountain” [Kent 78]

14. 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

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

16. 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

17. 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

18. 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

19. New York State Center of Excellence in Bioinformatics & Life Sciences R T U Assignment Read: –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 For next class (09/10/2007): –Give a short presentation about a similar problem in the domain of your major.