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PA TO and TO

PA TO and TO. Barry Smith.  HP:0001720 ! tachycardia =def. Process : GO:0060048 cardiac muscle contraction Quality: PATO:0000912 increased rate HP = Human Phenotype Ontology (Peter Robinson et al.) How good is PATO’s account of ‘increased rate’. rate.

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PA TO and TO

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  1. PATO and TO Barry Smith

  2.  HP:0001720 ! tachycardia =def. Process: GO:0060048 cardiac muscle contractionQuality: PATO:0000912 increased rate HP = Human Phenotype Ontology (Peter Robinson et al.) How good is PATO’s account of ‘increased rate’

  3. rate PATO: rate =def. a quality of a single process inhering in a bearer by virtue of the bearer’s occurrence per unit time Does not bring out the fact that a rate exists only when processes of the same type repeat in a sequence Better definition: rate =def. a relation between a series of processes of a given type and a time unit consisting in the number of times processes of that type repeat per unit time

  4. increased rate PATO: increased rate =def. a rate which is relatively high. ‘Increased rate’ as used in HP means: rate above some normal threshold defined for each particular kind of patient p has increased-rate relative to threshold n =def. p is a process & p has rate r per unit time & r is greater than n

  5. Consequence of this analysis • Tachycardia only exists if there is the sort of cyclical repetition of cardiac muscle contraction that is involved in the heart’s beating. • Thus Tachycardia is not a rate of cardiac musclecontraction • Rather, it is a rate of cardiac muscle contraction repetition.

  6. http://bioportal.bioontology.org/ontologies/50220

  7. Multiple Inheritance / Tangled Hierachy car is_a is_a blue car subcompactcar is_a is_a blue subcompact car

  8. Multiple Inheritance • is a source of errors • encourages laziness • serves as obstacle to integration with neighboring ontologies • because it hampers formulation of cross-product definitions

  9. How to avoid multiple inheritance? car is_a is_a blue car subcompactcar is_a is_a blue subcompact car

  10. How to avoid multiple inheritance? qualities things car color is_a is_a blue subcompactcar is_a things always instantiate the same universal; qualities can change from one time to the next dark blue

  11. How to avoid multiple inheritance? PATO OTTO car color is_a is_a blue subcompactcar is_a dark blue

  12. is_a relations are always permanently true car color is_a is_a blue subcompactcar is_a dark blue

  13. What is a stem length? 1. Abiotic stress trait =def. Response by the plant in terms of resistivity or sensitivity to abiotic stress. DISPOSITION 2. Plant height =def. A stature and vigor trait (TO:0000133) which is associated with the height of a whole plant (PO:0000003). Stature or vigor trait =def. A subjective assessment of the plant in similar site and growing conditions (often unfavorable conditions) based upon a specific facet of growth. CONFUSION 3. Anatomy and morphology trait =def. A plant trait (TO:0000387) which is associated with the anatomy or morphology of a plant anatomical entity (PO:0025131) or one or more constituent cellular components (GO:0005575) contained therein.

  14. X MEASUREMENT RESULT DISPOSITION X X

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