1. Function, Role, and Disposition in Basic Formal Ontology Robert Arp and Barry Smith Ontology Research Group (ORG) www.org.buffalo.edu National Center for Biomedical Ontology (NCBO) www.bioontology.org 1

2. FUNCTION, ROLE, AND DISPOSITION IN BASIC FORMAL ONTOLOGY ABSTRACT - Numerous research groups are now utilizing Basic Formal Ontology (BFO) as an upper-level framework to assist in the organization and integration of biomedical information. - This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and we consider the merits of recognizing two sub-categories of function, namely artifactual and biological function. - The motivation is to help advance the coherent treatment of functions, roles, and dispositions, to help provide the potential for more detailed classification, and to shed light on BFO’s general structure and use. 2

3. Basic Formal Ontology (BFO) 3

4. continuant entities - have continuous existence in time - preserve their identity through change - exist in toto, if they exist at all occurrent entities - have temporal parts - unfold themselves phase by phase - exist only in their phases/stages 4

5. continuant independent continuant object object boundary object aggregate fiat object part site dependent continuant generically dependent continuant specifically dependent continuant quality realizable entity function role disposition spatial region zero- dimensional region one- dimensional region two- dimensional region three- dimensional region continuant 5

6. occurrent processual entity process process boundary process aggregate fiat process part processual context spatiotemporal region scattered spatiotemporal region connected spatiotemporal region spatiotemporal instant spatiotemporal interval temporal region scattered temporal region connected temporal region temporal instant temporal interval occurrent 6

7. Some Ontologies Using BFO BioTop: A Biomedical Top-Domain Ontology Common Anatomy Reference Ontology (CARO) Foundational Model of Anatomy (FMA) Gene Ontology (GO) Infectious Disease Ontology (IDO) Ontology for Biomedical Investigations (OBI) Ontology for Clinical Investigations (OCI) Phenotypic Quality Ontology (PaTO) Protein Ontology (PRO) RNA Ontology (RnaO) Senselab Ontology Sequence Ontology (SO) Subcellular Anatomy Ontology (SAO) Vaccine Ontology (VO) 7

8. Some Ontologies Using BFO BFO now required for members of OBO Foundry (http://www.obofoundry.org/) 8

9. Blinding Flash of the Obvious continuant occurrent (always dependent on one or more independent continuants) independent continuant dependent continuant 9

10. BFO: The Very Top continuant occurrent (always dependent on one or more independent continuants) independent continuant dependent continuant object site quality function role disposition process processual context 10

11. BFO: The Very Top continuant independent continuant dependent continuant quality function role disposition In this presentation, we are concerned with 11

12. continuant independent continuant object object boundary object aggregate fiat object part site dependent continuant generically dependent continuant specifically dependent continuant quality realizable entity function role disposition spatial region zero- dimensional region one- dimensional region two- dimensional region three- dimensional region continuant 12

13. realizable entity -a dependent continuant -can be realized (manifested, actualized, executed) in an occurrent process function role disposition 13

14. realizable entity -periods of actualization, when being realized screwdriver is actually being used person is acting on stage water is rising in stem of flower -periods of dormancy, when exist but not realized screwdriver is in tool box president is on vacation breakable crystal vase function role disposition 14

15. function - realizable entity - has a bearer, which is an independent continuant - of a type instances of which typically have realizations (true for role and disposition, too) 15

16. function - the function of an individual entity is itself an individual entity - the function of your heart is not the same entity as the function of my heart - a function exists in virtue of the typical physical make-up of a bearer of this type - this physical make-up is something that bearer possesses because of how it came into being 16

17. function of liver: to store glycogen birth canal: to enable transport eye: to see Examples 17

18. - only parts of organisms have biological functions - typically each part has more than one function heart pumps blood and produces sounds mitochondrion makes ATP and signals cells 18

19. Possible new sub-categories in BFO - artifactual function - biological function 19

20. artifactual function - designed and made intentionally (typically by one or more human beings) to function in a certain way Erlenmeyer flask: to hold liquid hammer: to drive in nails screwdriver: to fasten screws fan: to circulate air Bunsen burner: to produce a flame 20 Examples

21. biological function - exists and has the physical structure it has as a result of the coordinated expression of that organism’s structural genes mitochondrion: to produce ATP liver: to store glycogen eye: to see wax-producing mirror gland of worker honey bee: to produce beeswax 21 Examples

22. role - played by a continuant entity because this entity is in some optional natural, social, or institutional set of circumstances - bearers can have more than one role person as student and staff member mitochondrion has role in mental disease and cardiac disease 22

23. role - is optional: an entity can have a role only if it has the physical make-up which makes possible its realization, but it can have the physical make-up without having the role - bearers can have more than one role person as student and staff member mitochondrion has role in mental disease and cardiac disease 23

24. role of some chemical compound: to serve as analyte in an experiment a dose of penicillin in human child: to treat a disease this bacteria in a primary host: to cause infection person as a student, surgeon, or surrogate Examples 24

25. The worker bee problem: Is the worker bee a role? Organisms can have roles. But, it seems as if the worker bee is genetically determined to function as a worker bee. With our definition of function, could we say that the worker bee has a function? Possibly, if: - we allow functions to be ascribed to certain whole organisms, instead of just parts - we allow the entire colony of bees to be an organism, and the worker bee is one of the parts 25

26. disposition consider the disposition of a crystal vase to break - occurs in virtue of the bearer’s physical make-up - essentially (invariably, definitely) causes a specific process or transformation in the bearer in which it inheres - under specific circumstances, and - in conjunction with the laws of nature 26

27. disposition consider the disposition of a crystal vase to break - occurs in virtue of the bearer’s physical make-up - invariably causes a specific process or transformation in the bearer in which it inheres under an associated range of specific circumstances 27

28. disposition of car windshield to break if struck with a sledgehammer moving at 100 feet per second cell to become diploid following mitosis magnet to produce an electrical field Examples 28

29. tendency (possible new category of BFO) consider the tendency of a hemophiliac to bleed a lot - occurs in virtue of the bearer’s physical ma - essentially (invariably, definitely) causes a specific process or transformation in the bearer in which it inheres - under specific circumstances, and - in conjunction with the laws of nature 29

30. tendency consider the tendency of a hemophiliac to bleed a lot - potentially, and not invariably, causes a specific process or transformation in the bearer in which it inheres - under specific circumstances, and - in conjunction with the laws of nature 30

31. tendency of humans: to die prematurely from chain smoking severely depressed persons: to be suicidal crime rates of cities: to rise in summer months Examples 31

32. continuant independent continuant dependent continuant generically dependent continuant specifically dependent continuant quality realizable entity function role disposition tendency spatial region continuant Possible new category of BFO? 32

33. the heart has the (or a) biological function to pump blood the flask has the artifactual function to hold liquid the person has the role of surrogate a portion of blood has the disposition to coagulate a portion of saliva has the tendency to cause plaque to harden on the teeth 33