1. PATO and TO Barry Smith

2. 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’

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 muscle contraction Rather, it is a rate of cardiac muscle contraction repetition.

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

11. Multiple Inheritance / Tangled Hierachy car subcompact car blue car blue subcompact car is_a 11 is_a

12. 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 12

13. How to avoid multiple inheritance? car subcompact car blue car blue subcompact car is_a 13 is_a

14. How to avoid multiple inheritance? car subcompact car blue is_a 14 is_a dark blue color qualitiesthings things always instantiate the same universal; qualities can change from one time to the next

15. How to avoid multiple inheritance? car subcompact car blue is_a 15 is_a dark blue color PATO OTTO

16. asserted ontologies (reference ontologies) car subcompact car blue is_a 16 is_a dark blue color changeable essential

17. is_a relations are always permanently true car subcompact car blue is_a 17 is_a dark blue color

18. syntactic class: blue subcompact = subcompact car which is blue car subcompact car blue blue subcompact is_a 18 is_a dark blue color

20. 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.

21. DISPOSITION MEASUREMENT RESULT X X X