Substance concentrationsas conditions for the realization

of dispositions

Janna Hastings1

Christoph Steinbeck1

Ludger Jansen2

Stefan Schulz3

1 European Bioinformatics Institute, UK 2 University of Rostock, Germany3 University Medical Center, Freiburg, Germany

04/12/2023 2

Problem

Ontologies make statements that are universally true

Dispositional properties specifywhat might occur

under the right circumstances

Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions

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Dispositions, functions

Increasingly important in biomedical ontologies as they allow functionally similar groupings for entities that are constitutionally dissimilar

Realization: the process in which the disposition is ‘fulfilled’

Realization is conditional

Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions

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Small molecule bioactivity

Drugs and metabolites: small molecules active in biological contexts

Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions

Image credit: gassama.myweb.uga.edu/

Oxygen transport in the bodydepends on the disposition of heme to bind oxygenand the disposition to release oxygen

depending on the surroundingconcentration

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Concentrations

Concentrations are system propertiesa concentration is always a concentration of something in something

Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions

Image credit: http://www.boat-ed.com/images/drawings/

e.g. the concentration of alcohol in blood

here shown in the Blood Alcohol Chart

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Active concentrations

Consider aspirin as treatment for a headache

Too few individual molecules will have no effectToo many tablets will have unpleasant additional effects

Image credit: tell.fll.purdue.edu

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Conditions in biomedical ontologies

Conditions for dispositional property realization, such as concentrations for active molecules, are seldom modelled explicitly in biomedical ontologies

Such models are difficult to express in OWL binary relations

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Dispositions are realized in processes

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Model: Dispositions

Consider the case of aspirin, which has the disposition to treat pain

We can formulate this as:

PortionOfAspirin ⊑ ∃ bearerOf.(Disposition ⊓ ∀ hasRealization.(Treating ⊓

∃ hasParticipant.Pain))

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Concentrations are properties of mixtures

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Model: Concentrations

Consider a mixture of 10g water with 10g glucose

We have three entities of interest (i) the water/glucose mixture wgmix,

(ii) the water fraction wcoll, i.e. the collection of all water molecules, and

(iii) the glucose fraction gcoll, i.e. the collection of all glucose molecules.

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Model: Concentrations

The collection of glucose molecules in the water:G EntireMolecule ⊑Gcoll HomogeneousCollection ⊑

Gcoll ≣ ∃ hasGranularPart.G ⊓ ∀ hasGranularPart.G

A mixture has several components:WGmix Mixture ⊑

WGmix =1 ⊑ hasComponent.Gcoll =1 ⊓ hasComponent.Wcoll

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Model: Concentrations

A concentration can be ascribed to a collection iff this collection is a component of a mixture

∃ bearerOf.Concentration ≡ Homogeneous collection ⊓ ∃componentOf.Mixture

Concentration ⊑ ∃ inheresIn. (HomogeneousCollection ⊓ ∃componentOf.Mixture)

Finally, we can state thatBloodGlucoseVolumeConcentration ≡ VolumeConcentration ⊓ ∃

inheresIn. (PortionOfGlucose ⊓ ∃ componentOf.PortionOfBlood)

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The process, which realizes the disposition of a collection of molecules, can only occur when a sufficient concentration is available

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Conditions for realization

How do we link the relevant conditions to the realization of dispositions? As a trigger:

PortionOfAspirin ⊑ ∃ bearerOf.(Disposition ⊓ ∀ hasRealization.(Treating ⊓ ∃ hasParticipant.Pain ⊓ ∃ hasTrigger. SufficientConcentration))

where, of course,

SufficientConcentration BloodAspirinVolumeConcentration.⊑

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Conclusions

• Dispositional properties are fundamental to functional classification in Bio-ontologies

• Dispositional properties are defined in terms of their realization, but often realization also depends on triggering conditions

• One such triggering condition is the concentration of bioactive substances in the body

Acknowledgements

Funding• BBSRC, grant agreement number

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

• the DFG, grant agreement number JA 1904/2-1, SCHU 2515/1-1 GoodOD (Good Ontology Design).