(define-ontology petri-dish ()
  (ontology-annotation !dc:creator "Alan Ruttenberg")
  (class !quality "snap:quality" :partial)
  (class !petri-dish-shape "We factor a petri dish made of plastic, as a piece of plastic that has a certain shape. This represents the shape." :partial !quality)
  (object-property !has_determinate_part 
		   "Determinate parthood e.g., the relation of the finger to the hand, in which a determinate number of parts (at any given time) are directly part of the whole, and in which removing one determinate part necessarily damages or diminishes the whole. (Rector, et al. PMID:16515892)"
		   (super !has_part))
  (object-property !has_part "ro:part_of")
  (object-property !has_grain "Granular parthood e.g., the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not necessarily damage or diminish the whole. (Rector, et al. PMID:16515892)")
  (object-property !has_determinate_part :transitive)
  (class !object "snap:object" :partial)
  (object-property !has_quality "subproperty of bears")
  (class !hydrocarbon_molecule "CHEBI:24632" :partial !object)
  (class !portion-of-plastic 
    "Anything which is made (solely) of plastic is a portion of plastic. For illustrative purposes  make the idealization that plastic only contains hydrocarbon molecules, which might be wrong. Determinate parts of a portion of plastic are portions of plastic themselves"
    :partial 
    (manch (and !object
		(all !has_determinate_part !portion-of-plastic)
		(some !has_grain !hydrocarbon_molecule)
		(all !has_grain !hydrocarbon_molecule))))
  (class !petri-dish
    "A plastic petri dish. In order to avoid multiple asserted inheritence, this is a defined class= those portions of plastic that have the right shape"
    :complete
	 (manch 
	  (and !portion-of-plastic
	       (some !has_quality !petri-dish-shape))))
  
  (individual !petri_dish_1
    "For testing purposes we create an instance of petri dish, and assert that it has a determinate part. We expect that the part will be classified as a portion of plastic if our definitions worked"
    (type !petri-dish)
    (value !has_determinate_part (individual !piece_of_petri_dish_1)))
  )

(define-ontology petri-dish-hurts ()
  (class !quality :partial)
  (class !petri-dish-shape :partial !quality)
  (object-property !has_determinate_part (inverse-of !determinate_part_of))
  (object-property !has_determinate_part (super !has_part))
  (object-property !has_part)
  (object-property !has_grain)
  (object-property !has_determinate_part :transitive)
  (class !object :partial)
  (object-property !has_quality)
  (class !hydrocarbon_molecule :partial !object)
  (class !portion-of-plastic :partial 
	 (manch (and !object
		     (all !has_determinate_part !portion-of-plastic)
		     (some !has_determinate_part !portion-of-plastic)
		     (some !has_grain !hydrocarbon_molecule)
		     (all !has_grain !hydrocarbon_molecule))))
  (individual !petri_dish_1 (type !petri-dish))
  (individual !piece_of_petri_dish_1 (value !determinate_part_of !petri_dish_1))
  (sub-class-of !portion-of-plastic
		(manch (some !determinate_part_of !portion-of-plastic)))
  (class !petri-dish :complete
	 (manch 
	  (and !portion-of-plastic
	       (some !has_quality !petri-dish-shape))))
  )