1 Why computer science needs philosophy Barry Smith National Center for Ontological Research

2 Shimon Edelman’s Riddle of Representation two humans, a monkey, and a robot are looking at a piece of cheese; what is common to the representational processes in their visual systems?

3 Answer: The cheese, of course

4 From chromosome to disease

5 genomics proteomics reactomics metabonomics phenomics behavioromics connectomics toxicopharmacogenomics … legacy of Human Genome Project

6 -omics data biochemical disease pathway data biomedical image data electronic health record data hospital management data hospital insurance data public health data Chinese chicken data

7 a vast new problem of the unity of science medical researchers, clinical practitioners, first responders, customs agencies, pharmaceutical companies, disease control centers need to communicate in ways which involve huge amounts of data

8 the prehistory of science

9 There is no problem of the unity of science because all science can be stored inside one person’s head

10 The era of empiricism: the problem of the unity of science is solved by reality itself

11 If two scientists disagree they resolve their disagreement by examining reality

12 the logical positivist interlude

13 A science is a collection of propositions (Bolzano: each science is identified with an ideal scientific textbook) The problem of the unity of science is a problem of logic

14 Science today relies ineluctably on the creation of databases and associated algorithms

16 genomics proteomics reactomics metabonomics phenomics behavioromics toxicopharmacogenomics … legacy of Human Genome Project

17 -omics data biochemical disease pathway data biomedical image data electronic health record data hospital management data hospital insurance data public health data Chinese chicken data

18 a vast new problem of communication medical researchers, clinical practitioners, first responders, customs agencies, pharmaceutical companies, disease control centers need to communicate in ways which involve huge amounts of data

19 The problem of the unity of science is a problem of computer science

22 To unify science it is enough to unify data UML Class Diagram

23 To solve the problem of the unity of science, what we need is an ‘information model’

24 A tragic example “Health Level 7 Reference Information Model” (HL7 RIM) – a standard for exchange of information between clinical information systems

25 HL7 RIM ‘a static model of health and health care information as viewed within the scope of HL7 standards development activities. It is the combined consensus view of information from the perspective of the HL7 working group and the HL7 international affiliates.’

26 The ultimate special purpose ontology A healthcare messaging system used as the basis for an entire clinical record architecture, extending as far as core genomic data Rather like using air-traffic control messaging as starting point for a science of airplane thermodynamics

27 HL7-RIM Animal Definition: A subtype of Living Subject representing any animal-of-interest to the Personnel Management domain. LivingSubject Definition: A subtype of Entity representing an organism or complex animal, alive or not.

28 Person Definition: A Living Subject representing single human being [sic] who is uniquely identifiable through one or more legal documents HL7-RIM

29 Katrina

30 Katrina

31 Person Definition: A Living Subject representing single human being [sic] who is uniquely identifiable through one or more legal documents HL7-RIM

32 Person is a subtype of LivingSubject LivingSubject is a subtype of Entity Definition of Entity: A physical thing, group of physical things or an organization capable of participating in Acts, while in a role.

33 States of Entity active: The state representing the fact that the Entity is currently active. inactive: The state representing the fact that an entity can no longer be an active participant in events. normal: The “typical” state. Excludes “nullified”, which represents the termination state of an Entity instance that was created in error nullified: The state representing the termination of an Entity instance that was created in error.

34 Persons are Entities What does ‘active’ and ‘inactive’ mean as applied to Person? Is there a special kind of death-through- nullification in the case of these instances of Person who were created in error? (The definitions of ‘active’ and ‘inactive’ provide no assistance in this regard.)

35 Persons are Entities What does ‘active’ and ‘inactive’ mean as applied to Person? Is there a special kind of death-through- nullification in the case of these instances of Person who were created in error? (The definitions of ‘active’ and ‘inactive’ provide no assistance in this regard.)

36 A Person is not a person ‘Person’ refers not to persons, but to objects in information systems – entities created through processes of data entry. They undergo not: processes such as being treated, falling ill, being born, dying, moving from place to place (the processes-of-interest in the domain of healthcare), but: processes of being revised, reactivated, nullified

37 yet Persons have postal addresses have ethnicities have marital status have educational level..

38 HL7’s backbone ‘Act’ class Act Definition: An Act is the record of an Act An X is the Y of an X “There is no difference between an activity and its documentation”

39 Logically Contradictory Definitions Definition of Act: An Act is an action of interest that has happened, can happen, is happening, is intended to happen, or is requested/demanded to happen. Definition of Act: An Act is the record of something that is being done, has been done, can be done, or is intended or requested to be done.

40 HL7 Incredibly Successful adopted by Oracle as basis for its Electronic Health Record technology; supported by IBM, GE, Sun... embraced as US federal standard central part of $18 billion program to integrate all UK hospital information systems

41 What’s gone wrong? People of good will are making mistakes because of lack of expertise Money is wasted on megasystems that cannot be used Methodology based on systematic use- mention confusions (sleeping is healthy and has 8 letters)

42 Ontologies (tech.) Standardized classification systems which enable data from different sources to be combined Ontology (phil.) The branch of metaphysics that deals with the nature of being.

43 ontologies are ambitious classification systems they rely on clear distinctions, for example between a name and its object and on theories of high-level categories such as function, process, thing, event, constituent if you want to build a good ontology … ASK AN ARISTOTELIAN PHILOSOPHER