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Processes and Properties


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Presented at the 2011 ISMB Bio-ontologies SIG. A detour into the difficulties of representing the properties of processes in ontologies, and some steps towar

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Processes and Properties

  1. 1. ISMB Bio-OntologiesSIG 2011<br />Processes and Properties<br />Colin Batchelor 1Janna Hastings 2,3<br />Christoph Steinbeck 2<br />1 Royal Society of Chemistry, Cambridge, UK<br />1Chemoinformatics and Metabolism, European Bioinformatics Institute, UK<br />2 Swiss Centre for Affective Sciences, University of Geneva, Switzerland<br />
  2. 2. How do we model the properties of processes?Rates of biochemical reactionsHeart rateSpeed of developmentWhat is the real effect of ‘regulation of heart rate’ (GO:0002027)We will work within the realist paradigm of the OBO community<br />Saturday, July 16, 2011<br />2<br />Processes and Properties (Bio-ontologies 2011)<br />
  3. 3. Continuants, occurrents and time<br />Occurrentsextend in time and have temporal parts <br />Continuants are fully present at each point in time that they exist at all, and their existence extends through time<br />Saturday, July 16, 2011<br />3<br />Processes and Properties (Bio-ontologies 2011)<br />
  4. 4. Qualities are dependent continuants<br />I have a height throughout my lifetime<br />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<br />Dependent entities must depend on independent entities<br />Saturday, July 16, 2011<br />4<br />Processes and Properties (Bio-ontologies 2011)<br />
  5. 5. Jones drove without a licence, without insurance, without lights after dark,<br />under the influence of alcohol and above the speed limit.<br />Which of these are properties of Jones, or Jones’s vehicle?<br />Which are properties of the driving?<br />And what about Jones’s heart rate?<br />
  6. 6. Properties of processes?<br />BFO admits no properties of processes beyond their boundaries and durations, as it does not allow second-order dependence<br />In GFO, there are process roles which can accommodate some properties<br />DOLCE explicitly allows for temporal qualities as properties of process<br />Saturday, July 16, 2011<br />6<br />Processes and Properties (Bio-ontologies 2011)<br />
  7. 7. Four kinds of is-a relation<br />
  8. 8. Discrete vs. Continuous<br />Saturday, July 16, 2011<br />8<br />Processes and Properties (Bio-ontologies 2011)<br />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.<br />benzothiadiazine<br />bendroflumethiazide<br />chlorothiazide<br />vs.<br />
  9. 9. Class intersection vs. class union<br />Class intersection involves differentiae that refer outside the definiendum.<br />electronic spectroscopy involves probing the electronic modes of atoms and molecules<br />ultraviolet spectroscopy uses ultraviolet light<br />Class union involves differentiae that refer within the definiendum.<br />red light is that which has a wavelength between 620 nm and 740 nm<br />You can have both, at least for dependent continuants and occurrents.<br />
  10. 10. What is heart rate? <br />Heart rate allows comparison between two different heart beating processes:<br />Process P can be more or less X than process P‘<br />To enable this comparison, X can be quantified (for a given temporal extent)<br />Saturday, July 16, 2011<br />10<br />Processes and Properties (Bio-ontologies 2011)<br />
  11. 11. How is heart rate different to speed?<br />Saturday, July 16, 2011<br />11<br />Processes and Properties (Bio-ontologies 2011)<br />How is heart rate <br />different from <br />speed? <br />Different parts p, p’ of a process P can have different values X, X‘ at times t, t’<br />
  12. 12. Saturday, July 16, 2011<br />12<br />Processes and Properties (Bio-ontologies 2011)<br />heart beating<br />is a<br />slow heart beating<br />normal heart beating<br />fast heart beating<br />instance of<br />The policeman’s heart beating<br />Jones’s heart beating<br />
  13. 13. Specialization<br />The is-a relation for process properties is specialization.<br />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.<br />
  14. 14. What does heart rate depend on?<br />The DOLCE approach would be to say something like: <br />heart rate depends_onheartbeatdepends_onheart <br />but if we follow BFO and disallow dependence chains then we get: <br />heart ratedepends_onregularly beating heart <br />and regularly beating heart is not a universal. <br />Saturday, July 16, 2011<br />14<br />Processes and Properties (Bio-ontologies 2011)<br />
  15. 15. What does heart rate depend on?<br />Saturday, July 16, 2011<br />15<br />Processes and Properties (Bio-ontologies 2011)<br />Jones’s Heart<br />The beating process that is taking placeright as Jones notices the policeman<br />Image credit: Patrick J. Lynch<br />
  16. 16. The life of Socrates substance-depends upon Socrates because it is part of the essence of his particular life that it happened to Socrates.<br />However, Socrates does not substance-depend upon his life because he might have had a different life.<br />But Socrates existentially depends on his particular life, because he couldn’t have existed without one.<br />heart rate substance_depends_onheart<br />you might have a different heart rate<br />heart rate existentially_depends_onheartbeat<br />the same heart rate might come from a<br />different heartbeat<br />heartbeat substance_depends_onheart<br />a given heart might have a different heartbeat<br />E. J. Lowe, Ontological Dependence,<br />The Stanford Encyclopedia of Philosophy<br />image: bencrowe, some rights reserved<br />
  17. 17. Classifying heart rates<br />heartbeat at 90 bpmequivalentTo heartbeat and has_process_quality90 bpm<br />OR<br />heartbeat at 90 bpmis_aheartbeat <br />heartbeat is_acyclical physiological process<br />Saturday, July 16, 2011<br />17<br />Processes and Properties (Bio-ontologies 2011)<br />
  18. 18. Conclusions<br />There are process qualities and they are occurrents. <br />Theyexistentially-depend on processes and substance-depend on the participants<br />They fit into a determinable-subsumptionhierarchy<br />Speed and acceleration, being wholly present at a single point in time, are conventional qualities. <br />Saturday, July 16, 2011<br />18<br />Processes and Properties (Bio-ontologies 2011)<br />
  19. 19. Acknowledgements<br />Funding<br />BBSRC, grant agreement number BB/G022747/1 within the "Bioinformatics and biological resources" fund <br />Saturday, July 16, 2011<br />19<br />Processes and Properties (Bio-ontologies 2011)<br />