Processes and Properties

Processes and Properties

Colin Batchelor 1

Janna Hastings 2,3

Christoph Steinbeck 2

1 Royal Society of Chemistry, Cambridge, UK1 Chemoinformatics and Metabolism, European Bioinformatics Institute, UK

2 Swiss Centre for Affective Sciences, University of Geneva, Switzerland

ISMB Bio-Ontologies SIG 2011

Wednesday, April 12, 2023 2Processes and Properties (Bio-ontologies 2011)

How do we model the properties of processes?

Rates of biochemical reactionsHeart rate

Speed of development

What is the real effect of ‘regulation of heart rate’ (GO:0002027)

We will work within the realist paradigm of the OBO community


Continuants, occurrents and time

Occurrents extend in time and have temporal parts

Continuants are fully present at each point in time that they exist at all,

and their existence extends through time


Qualities are dependent continuants

I have a height throughout my lifetime

My height is wholly present at each moment in time that it exists, which coincides which each

moment that I exist, as my height is dependent on me

Dependent entities must depend on independent entities

Jones drove without a licence, without insurance, without lights after dark,under the influence of alcohol and above the speed limit.

Which of these are properties of Jones, or Jones’s vehicle?Which are properties of the driving?And what about Jones’s heart rate?


Properties of processes?

BFO admits no properties of processes beyond their boundaries and durations, as it does not

allow second-order dependence

In GFO, there are process roles which can accommodate some properties

DOLCE explicitly allows for temporal qualities as properties of process

Four kinds of is-a relationIntersections Unions

Continuants

Genus subsumption

Class intersection: how we usually write formal definitions for continuants

Determinable subsumption

Class union: red is the union of scarlet, crimson, vermilion, pillarbox red, and so on and so forth

Occurrents

Specification

Class intersection: we can define processes based on their participants, outputs etc

Specialization

Careful and careless paintingFast and slow painting


Discrete vs. Continuous

benzothiadiazine

bendroflumethiazide chlorothiazide

Heterocyclic compound of a ring with sulfur and two nitrogen atoms fused to a benzene ring. Members inhibit sodium-potassium-chloride symporters and are used as diuretics.

vs.

Class intersection vs. class union

Class intersection involves differentiae that refer outside the definiendum.

– electronic spectroscopy involves probing the electronic modes of atoms and molecules

– ultraviolet spectroscopy uses ultraviolet light

Class union involves differentiae that refer within the definiendum.

– red light is that which has a wavelength between 620 nm and 740 nm

You can have both, at least for dependent continuants and occurrents.


What is heart rate?

Heart rate allows comparison between two different heart beating processes:

Process P can be more or less X than process P‘

To enable this comparison, X can be quantified (for a given temporal extent)


How is heart rate different to speed?How is heart rate different from speed?

Different parts p, p’ of a process P can have different values X, X‘ at times t, t’


heart beating

slow heart beating

normal heart beating fast heart beating

The policeman’s heart beating

Jones’s heart beating

instance of

is a

Specialization

The is-a relation for process properties is specialization.

fast heartbeat is the union of heartbeat at 120 bpm, 121 bpm, 122 bpm, 123 bpm, points in between, and so on and so forth.


What does heart rate depend on?The DOLCE approach would be to say something like:

heart rate depends_on heartbeat depends_on heart

but if we follow BFO and disallow dependence chains then we get:

heart rate depends_on regularly beating heart

and regularly beating heart is not a universal.


What does heart rate depend on?

Image credit: Patrick J. Lynch

Jones’s Heart

The beating process that is taking placeright as Jones notices the policeman

The life of Socrates substance-depends upon Socrates because it is part of the essence of his particular life that it happened to Socrates.

However, Socrates does not substance-depend upon his life because he might have had a different life.

But Socrates existentially depends on his particular life, because he couldn’t have existed without one.heart rate substance_depends_on heartyou might have a different heart rate

heart rate existentially_depends_on heartbeatthe same heart rate might come from adifferent heartbeat

heartbeat substance_depends_on hearta given heart might have a different heartbeat

E. J. Lowe, Ontological Dependence,The Stanford Encyclopedia of Philosophy

image: bencrowe, some rights reserved


Classifying heart rates

heartbeat at 90 bpm equivalentTo heartbeat and has_process_quality 90 bpm

OR

heartbeat at 90 bpm is_a heartbeat heartbeat is_a cyclical physiological process


ConclusionsThere are process qualities and they are occurrents.

They existentially-depend on processes and substance-depend on the participants

They fit into a determinable-subsumption hierarchy

Speed and acceleration, being wholly present at a single point in time, are conventional qualities.

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Acknowledgements

FundingBBSRC, grant agreement number

BB/G022747/1 within the "Bioinformatics and biological resources" fund

Processes and Properties (Bio-ontologies 2011)

Health & Medicine

Processes and Properties