BFO and Disease

Barry Smith8/19.2012

A Chart representing how John’s temperature

changes

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A Chart representing how John’s temperature

changes

3

John’s temperature,the temperature he has throughout his entire life, cycles through different determinate temperatures from one time to the next

John’s temperature is a physiology variable which, in thus changing, exerts an influence on other physiology variables through time

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BFO: The Very Top

continuant

independentcontinuant

dependentcontinuant

quality

occurrent

temperature 5

Blinding Flash of the Obvious

independentcontinuant

dependentcontinuant

quality

temperature types

instances

organism

John John’s

temperature 6

Blinding Flash of the Obvious

independentcontinuant

dependentcontinuant

quality

temperature types

instances

organism

John John’s

temperature 7

Blinding Flash of the Obvious

temperature types

instances

organism

John John’s

temperature .

8

inheres_in

temperature types

instances

John’s temperature

9

37ºC37.1º

C37.5º

C37.2º

C37.3º

C37.4º

C

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6

human types

instances

John

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embryo

fetus adultneonat

einfant child

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6

Temperature subtypesDevelopment-stage

subtypes

are threshold divisions (hence we do not have sharp boundaries, and we have a certain degree of choice, e.g. in how many subtypes to distinguish, though not in their ordering)

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independentcontinuant

dependentcontinuant

quality

temperature types

instances

organism

John John’s

temperature

12

independentcontinuant

dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

course of temperature

changes

John’s temperature history

13

independentcontinuant

dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

temperature process profile

John’s temperature history

independentcontinuant

dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

life of an organism

John’s life

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BFO: The Very Top

continuant occurrent

independentcontinuant

dependentcontinuant

quality disposition

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Disposition- of a glass vase, to shatter if dropped- of a human, to eat - of a banana, to ripen- of John, to lose hair

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Dispositionif it ceases to exist, then its bearer and/or its immediate surrounding environment is physically changedits realization occurs when its bearer is in some special physical circumstancesits realization is what it is in virtue of the bearer’s physical make-up

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:.

Function - of liver: to store glycogen- of birth canal: to enable transport- of eye: to see- of mitochondrion: to produce ATP

functions are dispositions which are designed or selected for

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independentcontinuant

dependentcontinuant

function

to seeeye

John’s eye function of John’s eye: to see

occurrent

process

process of seeing

John seeing

20

OGMSOntology for General Medical

Science

http://code.google.com/p/ogms

21

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Physical Disorder

:.

Physical Disorder

– independent continuant

fiat object part

A causally linked combination of physical components of the extended organism that is clinically abnormal.

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Clinically abnormal

– (1) not part of the life plan for an organism of the relevant type (unlike aging or pregnancy),

– (2) causally linked to an elevated risk either of pain or other feelings of illness, or of death or dysfunction, and

– (3) such that the elevated risk exceeds a certain threshold level.*

*Compare: baldness

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Realizable dependent continuants

Role: nurse role, pathogen role, food role

Disposition: fragility, virulence, susceptibility, genetic disposition to disease X

Function: to pump (of the heart), to unlock (of the key)

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Role (Externally-Grounded Realizable Entity)

role =def. a realizable entity• which exists because the bearer is in

some special physical, social, or institutional set of circumstances in which the bearer does not have to be, and

• is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed.

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Disposition (Internally-Grounded Realizable Entity)

disposition =def.

a realizable entity which if it ceases to exist, then its bearer is physically changed, and

whose realization occurs when this bearer is in some special physical circumstances, in virtue of the bearer’s physical make-up

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Function (A Disposition Designed or Selected For)

function =def.

a disposition that

exists in virtue of the bearer’s physical make-up,,

and

this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain kind.

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Four distinct classificatory tasks

1. of people (patients, carriers, …)

2. of diseases (cases, instances, problems, …)

3. of courses of disease (symptoms, treatments…)

4. of representations (records, observations, data, diagnoses…)

ICD confuses 1. & 2.

HL7, most standard terminologies, confuse 2. and 4

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Four distinct BFO categories

1. person (patient, carrier, …) – independent continuant

2. disease (case, instance, problem, …) – specifically dependent continuant

3. course of disease (symptom, treatment…)– occurrent

4. representation (record, datum, diagnosis…)– generically dependent continuant

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Four distinct BFO categories

1. people (patients, carriers, …) – independent continuants

2. disease (case, instance, problem, condition …) – disposition

3. course of disease (symptom, episode, outbreak …)– realization of dispositions

4. representations (records, data, diagnoses…)– generically dependent continuants

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Disposition

Internally-Grounded Realizable Entity

A disposition is

a realizable entity which is such that, if it ceases to exist, then its bearer is physically changed,

whose realization occurs, in virtue of the bearer’s physical make-up, when this bearer is in some special physical circumstances

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Disorder

1. person

– independent continuantobjects

fiat object part

object aggregate

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Disorder

A fiat object part of an organism which serves as the bearer of a disposition of a certain sort

This fiat object may have no determinate boundaries

(compare: Downtown Santa Barbara)

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Where does Mount Everest begin and end?Cf. Barry Smith and David M. Mark, “Do Mountains Exist?”, Environment and Planning B, 30, 2003.

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Big Picture (with thanks to Richard Scheuermann)

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A disease is a disposition rooted in a

physical disorder in the organism and

realized in pathological processes.

etiological process

produces

disorder

bears

disposition

realized_in

pathological process

produces

abnormal bodily features

recognized_as

signs & symptomsinterpretive process

produces

diagnosis

used_in37

Elucidation of Primitive Terms ‘bodily feature’ - an abbreviation for a physical

component, a bodily quality, or a bodily process. disposition - an attribute describing the propensity to

initiate certain specific sorts of processes when certain conditions are satisfied.

clinically abnormal - some bodily feature that (1) is not part of the life plan for an organism of the

relevant type (unlike aging or pregnancy), (2) is causally linked to an elevated risk either of pain or

other feelings of illness, or of death or dysfunction, and (3) is such that the elevated risk exceeds a certain threshold

level.*

*Compare: baldness38

Definitions - Foundational Terms

Disorder =def. – A causally linked combination of physical components that is clinically abnormal.

Pathological Process =def. – A bodily process that is a manifestation of a disorder and is clinically abnormal.

Disease =def. – A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.

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Dispositions and Predispositions

All diseases are dispositions; not all dispositions are diseases.

A predisposition is a disposition. Predisposition to Disease of Type X =def. – A disposition

in an organism that constitutes an increased risk of the organism’s subsequently developing the disease X.

HNPCC is caused by a disorder (mutation) in a DNA mismatch repair gene that disposes to the acquisition of additional mutations from

defective DNA repair processes, and thus is a predisposition to the development of colon cancer.

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Definitions - Clinical Evaluation Terms

Sign =def. – A bodily feature of a patient that is observed in a physical examination and is deemed by the clinician to be of clinical significance. (Objectively observable features)

Symptom =def. – A experienced bodily feature of a patient that is observed by and observable only by the patient and is of the type that can be hypothesized by a patient to be a realization of a disease. (A restricted family of phenomena including pain, nausea, anger, drowsiness, which are of their nature experienced in the first person)

Symptoms are subjective. But this does not mean that there is no objective fact of the matter whether a given symptom exists

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Cirrhosis - environmental exposure

Etiological process - phenobarbitol-induced hepatic cell death produces

Disorder - necrotic liver bears

Disposition (disease) - cirrhosis realized_in

Pathological process - abnormal tissue repair with cell proliferation and fibrosis that exceed a certain threshold; hypoxia-induced cell death produces

Abnormal bodily features recognized_as

Symptoms - fatigue, anorexia Signs - jaundice, splenomegaly

Symptoms & Signs used_in

Interpretive process produces

Hypothesis - rule out cirrhosis suggests

Laboratory tests produces

Test results - elevated liver enzymes in serum used_in

Interpretive process produces

Result - diagnosis that patient X has a disorder that bears the disease cirrhosis

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Influenza - infectious

Etiological process - infection of airway epithelial cells with influenza virus produces

Disorder - viable cells with influenza virus bears

Disposition (disease) - flu realized_in

Pathological process - acute inflammation produces

Abnormal bodily features recognized_as

Symptoms - weakness, dizziness Signs - fever

Symptoms & Signs used_in

Interpretive process produces

Hypothesis - rule out influenza suggests

Laboratory tests produces

Test results - elevated serum antibody titers used_in

Interpretive process produces

Result - diagnosis that patient X has a disorder that bears the disease flu

But the disorder also induces normal physiological processes (immune response) that can results in the elimination of the disorder (transient disease course).

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Huntington’s Disease - genetic Etiological process - inheritance of

>39 CAG repeats in the HTT gene produces

Disorder - chromosome 4 with abnormal mHTT bears

Disposition (disease) - Huntington’s disease realized_in

Pathological process - accumulation of mHTT protein fragments, abnormal transcription regulation, neuronal cell death in striatum produces

Abnormal bodily features recognized_as

Symptoms - anxiety, depression Signs - difficulties in speaking and

swallowing

Symptoms & Signs used_in

Interpretive process produces

Hypothesis - rule out Huntington’s suggests

Laboratory tests produces

Test results - molecular detection of the HTT gene with >39CAG repeats used_in

Interpretive process produces

Result - diagnosis that patient X has a disorder that bears the disease Huntington’s disease

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HNPCC - genetic pre-disposition

Etiological process - inheritance of a mutant mismatch repair gene produces

Disorder - chromosome 3 with abnormal hMLH1 bears

Disposition (disease) - Lynch syndrome realized_in

Pathological process - abnormal repair of DNA mismatches produces

Disorder - mutations in proto-oncogenes and tumor suppressor genes with microsatellite repeats (e.g. TGF-beta R2) bears

Disposition (disease) - non-polyposis colon cancer realized in

Symptoms (including pain)

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Arterial AneurysmDisposition – atherosclerosis

realized inPathological process – fatty material collects within the walls of arteries

producesDisorder – artery with weakened wall

bearsDisposition – of artery to become distended

realized_inPathological process – process of distending

producesDisorder – arterial aneurysm

bearsDisposition – of artery to rupture

realized inPathological process – (catastrophic event) of rupturing

producesDisorder – ruptured artery, arterial system with dangerously low blood pressure

bearsDisposition – circulatory failure

realized inPathological process – exsanguination, failure of homeostasis

producesDeath 46

Definition: Etiology

Etiological Process =def. – A process in an organism that leads to a subsequent disorder.

Example: toxic chemical exposure resulting in a mutation in the genomic DNA of a cell; infection of a human with a pathogenic virus; inheritance of two defective copies of a metabolic gene

The etiological process creates the physical basis of that disposition to pathological processes which is the disease.

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Definitions - Diagnosis

Clinical Picture =def. – A representation of a clinical phenotype that is inferred from the combination of laboratory, image and clinical findings about a given patient.

Diagnosis =def. – A conclusion of an interpretive process that has as input a clinical picture of a given patient and as output an assertion to the effect that the patient has a disease of such and such a type.

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Definitions - Qualities

Manifestation of a Disease =def. – A bodily feature of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable. Observability includes observable through elicitation of response or

through the use of special instruments. Preclinical Manifestation of a Disease =def. – A

manifestation of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination.

Clinical Manifestation of a Disease =def. – A manifestation of a disease that is detectable in a clinical history taking or physical examination.

Phenotype =def. – A (combination of) bodily feature(s) of an organism determined by the interaction of its genetic make-up and environment.

Clinical Phenotype =def. – A clinically abnormal phenotype. 49