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Substance concentrations as conditions for the realization of dispositions
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Substance concentrations as conditions for the realization of dispositions

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Presented at the ISMB 2010 Bio-ontologies SIG

Presented at the ISMB 2010 Bio-ontologies SIG

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    Substance concentrations as conditions for the realization of dispositions Substance concentrations as conditions for the realization of dispositions Presentation Transcript

    • Substance concentrationsas conditions for the realizationof dispositions
      Janna Hastings1
      Christoph Steinbeck1
      Ludger Jansen2
      Stefan Schulz3
      1 European Bioinformatics Institute, UK 2 University of Rostock, Germany
      3 University Medical Center, Freiburg, Germany
    • Problem
      Ontologies make statements that are universally true
      Dispositional properties specifywhat might occurunder the right circumstances
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      2
      Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions
    • 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
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      3
      Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions
    • Small molecule bioactivity
      Drugs and metabolites: small molecules active in biological contexts
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      4
      Oxygen transport in the bodydepends on the disposition of hemeto bind oxygen
      and the disposition to release oxygen
      depending on the surrounding
      concentration
      Image credit: gassama.myweb.uga.edu/
      Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions
    • Concentrations
      Concentrations are system propertiesa concentration is always a concentration of something in something
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      e.g. the concentration of alcohol in bloodhere shown in the Blood Alcohol Chart
      Image credit: http://www.boat-ed.com/images/drawings/
      Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions
      5
    • Active concentrations
      Consider aspirin as treatment for a headache
      Too few individual molecules will have no effectToo many tablets will have unpleasant additional effects
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      Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions
      6
      Image credit: tell.fll.purdue.edu
    • 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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      Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions
      7
    • Dispositions are realized in processes
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      Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions
      8
    • 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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      Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions
      9
    • Concentrations are properties of mixtures
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      Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions
      10
    • Model: Concentrations
      Consider a mixture of 10g water with 10g glucose
      We have three entities of interest
      the water/glucose mixture wgmix,
      the water fraction wcoll, i.e. the collection of all water molecules, and
      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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      12
    • 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 that
      BloodGlucoseVolumeConcentration ≡ VolumeConcentration ⊓ ∃ inheresIn. (PortionOfGlucose ⊓ ∃ componentOf.PortionOfBlood)
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      13
    • The process, which realizes the disposition of a collection of molecules, can only occur when a sufficient concentration is available
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      Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions
      14
    • 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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      Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions
      15
    • 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
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      Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions
      16
    • 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).