Substance concentrationsas conditions for the realizationof dispositions<br />Janna Hastings1<br />Christoph Steinbeck1<br...
Problem<br />Ontologies make statements that are universally true<br />Dispositional properties specifywhat might occurund...
Dispositions, functions<br />Increasingly important in biomedical ontologies as they allow functionally similar groupings ...
Small molecule bioactivity<br />Drugs and metabolites: small molecules active in biological contexts<br />7/5/2010<br />4<...
Concentrations<br />Concentrations are system propertiesa concentration is always a concentration of something in somethin...
Active concentrations<br />Consider aspirin as treatment for a headache<br />Too few individual molecules will have no eff...
Conditions in biomedical ontologies<br />Conditions for dispositional property realization, such as concentrations for act...
Dispositions are realized in processes<br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions for ...
Model: Dispositions<br />Consider the case of aspirin, which has the disposition to treat pain<br />We can formulate this ...
Concentrations are properties of mixtures<br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions f...
Model: Concentrations<br />Consider a mixture of 10g water with 10g glucose<br />We have three entities of interest <br />...
Model: Concentrations<br />The collection of glucose molecules in the water:<br />G ⊑ EntireMolecule<br />Gcoll ⊑ Homogene...
Model: Concentrations<br />A concentration can be ascribed to a collection iff this collection is a component of a mixture...
The process, which realizes the disposition of a collection of molecules, can only occur when a sufficient concentration i...
Conditions for realization<br />How do we link the relevant conditions to the realization of dispositions? As a trigger:<b...
Conclusions<br />Dispositional properties are fundamental to functional classification in Bio-ontologies<br />Dispositiona...
Acknowledgements<br />Funding<br />BBSRC, grant agreement number BB/G022747/1 within the "Bioinformatics and biological re...
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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

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Substance concentrations as conditions for the realization of dispositions

  1. 1. Substance concentrationsas conditions for the realizationof dispositions<br />Janna Hastings1<br />Christoph Steinbeck1<br />Ludger Jansen2<br />Stefan Schulz3<br />1 European Bioinformatics Institute, UK 2 University of Rostock, Germany<br />3 University Medical Center, Freiburg, Germany<br />
  2. 2. Problem<br />Ontologies make statements that are universally true<br />Dispositional properties specifywhat might occurunder the right circumstances<br />7/5/2010<br />2<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />
  3. 3. Dispositions, functions<br />Increasingly important in biomedical ontologies as they allow functionally similar groupings for entities that are constitutionally dissimilar<br />Realization: the process in which the disposition is ‘fulfilled’<br />Realization is conditional<br />7/5/2010<br />3<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />
  4. 4. Small molecule bioactivity<br />Drugs and metabolites: small molecules active in biological contexts<br />7/5/2010<br />4<br />Oxygen transport in the bodydepends on the disposition of hemeto bind oxygen<br />and the disposition to release oxygen<br />depending on the surrounding<br />concentration <br />Image credit: gassama.myweb.uga.edu/ <br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />
  5. 5. Concentrations<br />Concentrations are system propertiesa concentration is always a concentration of something in something<br />7/5/2010<br />e.g. the concentration of alcohol in bloodhere shown in the Blood Alcohol Chart<br />Image credit: http://www.boat-ed.com/images/drawings/ <br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />5<br />
  6. 6. Active concentrations<br />Consider aspirin as treatment for a headache<br />Too few individual molecules will have no effectToo many tablets will have unpleasant additional effects <br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />6<br />Image credit: tell.fll.purdue.edu<br />
  7. 7. Conditions in biomedical ontologies<br />Conditions for dispositional property realization, such as concentrations for active molecules, are seldom modelled explicitly in biomedical ontologies<br />Such models are difficult to express in OWL binary relations<br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />7<br />
  8. 8. Dispositions are realized in processes<br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />8<br />
  9. 9. Model: Dispositions<br />Consider the case of aspirin, which has the disposition to treat pain<br />We can formulate this as:<br />PortionOfAspirin ⊑ ∃ bearerOf.(Disposition ⊓ ∀ hasRealization.(Treating ⊓ ∃ hasParticipant.Pain))<br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />9<br />
  10. 10. Concentrations are properties of mixtures<br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />10<br />
  11. 11. Model: Concentrations<br />Consider a mixture of 10g water with 10g glucose<br />We have three entities of interest <br />the water/glucose mixture wgmix, <br />the water fraction wcoll, i.e. the collection of all water molecules, and <br />the glucose fraction gcoll, i.e. the collection of all glucose molecules. <br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />11<br />
  12. 12. Model: Concentrations<br />The collection of glucose molecules in the water:<br />G ⊑ EntireMolecule<br />Gcoll ⊑ HomogeneousCollection<br />Gcoll ≣ ∃ hasGranularPart.G ⊓ ∀ hasGranularPart.G<br />A mixture has several components:<br />WGmix ⊑ Mixture <br />WGmix ⊑ =1 hasComponent.Gcoll ⊓ =1 hasComponent.Wcoll<br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />12<br />
  13. 13. Model: Concentrations<br />A concentration can be ascribed to a collection iff this collection is a component of a mixture<br />∃ bearerOf.Concentration ≡ Homogeneous collection ⊓ ∃ componentOf.Mixture<br />Concentration ⊑ ∃ inheresIn. (HomogeneousCollection ⊓ ∃ componentOf.Mixture)<br />Finally, we can state that<br />BloodGlucoseVolumeConcentration ≡ VolumeConcentration ⊓ ∃ inheresIn. (PortionOfGlucose ⊓ ∃ componentOf.PortionOfBlood)<br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />13<br />
  14. 14. The process, which realizes the disposition of a collection of molecules, can only occur when a sufficient concentration is available<br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />14<br />
  15. 15. Conditions for realization<br />How do we link the relevant conditions to the realization of dispositions? As a trigger:<br />PortionOfAspirin ⊑ ∃ bearerOf.(Disposition ⊓ ∀ hasRealization.(Treating ⊓ ∃ hasParticipant.Pain ⊓ ∃ hasTrigger. SufficientConcentration)) <br />where, of course, <br />SufficientConcentration⊑ BloodAspirinVolumeConcentration.<br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />15<br />
  16. 16. Conclusions<br />Dispositional properties are fundamental to functional classification in Bio-ontologies<br />Dispositional properties are defined in terms of their realization, but often realization also depends on triggering conditions<br />One such triggering condition is the concentration of bioactive substances in the body<br />7/5/2010<br />Bio-ontologies 2010: Substance concentrations as conditions for the realization of dispositions<br />16<br />
  17. 17. Acknowledgements<br />Funding<br />BBSRC, grant agreement number BB/G022747/1 within the "Bioinformatics and biological resources" fund; and <br />the DFG, grant agreement number JA 1904/2-1, SCHU 2515/1-1 GoodOD (Good Ontology Design). <br />

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