1. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U MHI501 – Introduction to Health Informatics Key Challenges for MHI in making data understandable to computers SUNY at Buffalo - December 5, 2007 Werner CEUSTERS Center of Excellence in Bioinformatics and Life Sciences University at Buffalo, NY, USA http://www.org.buffalo.edu/RTU

2. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Ultimate goal A digital copy of the world

3. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The requirements are the challenges R1:A faithful representation of reality R2… of everything that is digitally registered, what is generic  scientific theories what is specific  what individual entities exist and how they relate R3:… throughout reality’s entire history, R4… which is computable in order to … … allow queries over the world’s past and present, … make predictions, … fill in gaps, … identify mistakes,...

4. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U In fact … the ultimate crystal ball

5. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The ‘binding’ wall How to do it right ?

6. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The requirements are the challenges R1:A faithful representation of reality R2… of everything that is digitally registered, what is generic  scientific theories what is specific  what individual entities exist and how they relate R3:… throughout reality’s entire history, R4… which is computable in order to … … allow queries over the world’s past and present, … make predictions, … fill in gaps, … identify mistakes,...

7. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U R1: A faithful representation of reality … … recognizes three levels: 1.The (first order) reality which exists ‘as it is’ prior to a cognitive agent’s perception thereof; 2.the cognitive representations of this reality embodied in observations and interpretations on the part of cognitive agents; 3.the publicly accessible concretizations constructed through cognitive insights as artifacts representing first order reality of which ontologies, terminologies and data repositories are examples. 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

8. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Get down that wall Granular Partition Theory: relates the copy to reality. Basic Formal Ontology: teaches us how to build an adequate grid.

9. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U But … This is not part of mainstream thinking Dominant prevailing paradigm: –Focus on ‘concepts’ (and don’t ask what ‘concepts’ actually are) –Leave it to computer scientists and data modeling consultants

10. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The requirements are the challenges R1:A faithful representation of reality R2… of everything that is digitally registered, what is generic  scientific theories what is specific  what individual entities exist and how they relate R3:… throughout reality’s entire history, R4… which is computable in order to … … allow queries over the world’s past and present, … make predictions, … fill in gaps, … identify mistakes,...

11. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The reality: a digital copy of part of the world Applying the grid does not give a distorted representation of reality, but only an incomplete representation !!!

12. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Key issue: keeping track of what the bits denote

13. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Key issue: keeping track of what the bits denote Images are no good: –Are too complex particulars in their own right that stand in another sort of relation to the part of reality that they depict. Terms / names ? Middle-East Madagascar Katrina

14. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Names are inadequate representational units “JFK”“Enola Gay” “Barry Smith”“George Bush”

15. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U IUI: Instance Unique Identifiers 5241 89023 109427 denotes Relationship managed in the RTS

16. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Referent Tracking System Components Referent Tracking Software Manipulation of statements about facts and beliefs Referent Tracking Datastore: IUI repository A collection of globally unique singular identifiers denoting particulars Referent Tracking Database A collection of facts and beliefs about the particulars denoted in the IUI repository Manzoor S, Ceusters W, Rudnicki R. Implementation of a Referent Tracking System. International Journal of Healthcare Information Systems and Informatics 2007;2(4):41-58.

17. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U But … Not yet tested in real life Difficult to understand Societal barriers: –Big Brother complex –N(ot) I(nvented) H(ere) syndrome –Publication bias

18. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The requirements are the challenges R1:A faithful representation of reality R2… of everything that is digitally registered, what is generic  scientific theories what is specific  what individual entities exist and how they relate R3:… throughout reality’s entire history, R4… which is computable in order to … … allow queries over the world’s past and present, … make predictions, … fill in gaps, … identify mistakes,...

19. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Eternal memory

20. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U Accept that everything may change: 1.changes in the underlying reality: Particulars come, change and go 2.changes in our (scientific) understanding: The plant Vulcan does not exist 3.reassessments of what is considered to be relevant for inclusion (notion of purpose). 4.encoding mistakes introduced during data entry or ontology development.

21. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U But … Current computational and representational facilities are unsatisfactory

22. New York State Center of Excellence in Bioinformatics & Life Sciences R T U New York State Center of Excellence in Bioinformatics & Life Sciences R T U The requirements are the challenges R1:A faithful representation of reality R2… of everything that is digitally registered, what is generic  scientific theories what is specific  what individual entities exist and how they relate R3:… throughout reality’s entire history, R4… which is computable in order to … … allow queries over the world’s past and present, … make predictions, … fill in gaps, … identify mistakes,...