processes and properties
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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
Wednesday, April 12, 2023 3Processes and Properties (Bio-ontologies 2011)
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
Wednesday, April 12, 2023 4Processes and Properties (Bio-ontologies 2011)
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?
Wednesday, April 12, 2023 6Processes and Properties (Bio-ontologies 2011)
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
Wednesday, April 12, 2023 8Processes and Properties (Bio-ontologies 2011)
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.
Wednesday, April 12, 2023 10Processes and Properties (Bio-ontologies 2011)
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)
Wednesday, April 12, 2023 11Processes and Properties (Bio-ontologies 2011)
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’
Wednesday, April 12, 2023 12Processes and Properties (Bio-ontologies 2011)
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.
Wednesday, April 12, 2023 14Processes and Properties (Bio-ontologies 2011)
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.
Wednesday, April 12, 2023 15Processes and Properties (Bio-ontologies 2011)
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
Wednesday, April 12, 2023 17Processes and Properties (Bio-ontologies 2011)
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
Wednesday, April 12, 2023 18Processes and Properties (Bio-ontologies 2011)
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.
Wednesday, April 12, 2023 19
Acknowledgements
FundingBBSRC, grant agreement number
BB/G022747/1 within the "Bioinformatics and biological resources" fund
Processes and Properties (Bio-ontologies 2011)
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