Function, Role, and Function, Role, and Disposition inDisposition in

Basic Formal OntologyBasic Formal OntologyRobert Arp and Barry Smith

Ontology Research Group (ORG)www.org.buffalo.edu

National Center for Biomedical Ontology (NCBO)www.bioontology.org

1

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

Basic Formal Basic Formal Ontology (BFO)Ontology (BFO)

3

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

continuant

5

occurrent

6

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 OntologySequence Ontology (SO)Subcellular Anatomy Ontology (SAO) Vaccine Ontology (VO)

7

Some Ontologies Using BFO

BFO now required formembers of

OBO Foundry

(http://www.obofoundry.org/)

8

Blinding Flash of the Obvious

continuant occurrent

(always dependent

on one or more independent continuants)

independentcontinuant

dependentcontinuant

9

BFO: The Very Top

continuant occurrent

(always dependent

on one or more independent continuants)

independentcontinuant

dependentcontinuant

objectsite

qualityfunctionroledisposition

processprocessual context

10

BFO: The Very Top

continuant

independentcontinuant

dependentcontinuant

qualityfunctionroledisposition

In thispresentation,

we areconcerned

with

11

continuant

12

realizable entity- a dependent continuant- can be realized (manifested,

actualized, executed)in an occurrentprocess

functionroledisposition

13

realizable entity- periods of actualization, when being realized

screwdriver is actually being usedperson is acting on stagewater is rising in stem of flower

- periods of dormancy, when exist but not realizedscrewdriver is in tool boxpresident is on vacationbreakable crystal vase

functionroledisposition

14

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

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 being16

function of

liver: to store glycogen

birth canal: to enable transport

eye: to see

Examples

17

- only parts of organisms have biological functions

- typically each part has more than one function

heart pumps blood and produces soundsmitochondrion makes ATP and signals cells

18

Possible new sub-categories in BFO

- artifactual function- biological function

19

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

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

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

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 roleperson as student and staff membermitochondrion has role in mental disease

and cardiac disease23

role ofsome 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

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

dispositionconsider 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

dispositionconsider 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

disposition ofcar windshield to break if struck with a sledgehammer moving at 100 feet per secondcell to become diploid following mitosismagnet to produce an electrical field

Examples

28

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

tendencyconsider 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

tendency ofhumans: to die prematurely from

chain smokingseverely depressed persons: to be

suicidalcrime rates of cities: to rise in summer months

Examples

31

continuant

Possible new category of

BFO?

32

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 surrogatea portion of blood has the disposition to

coagulatea portion of saliva has the tendency to cause plaque to harden on the teeth

33