(defvar *small-piece-of-go* 
  '(!go:GO_0000060
    (!go:GO_0000189 !go:GO_0000201 !go:GO_0000208)
    !go:GO_0007184
    !go:GO_0007262
    (!go:GO_0035105 !go:GO_0006993)))

(define-ontology type-hierarchy ()
  (value-partition *small-piece-of-go* :disjoint nil :covering nil))
		   
(define-ontology existential-hierarchy ()
  (object-property !go:go_isa :transitive )
  (existential-hierarchy !go:go_isa *small-piece-of-go* )
  (class !go:probe :complete (restriction !go:go_isa (some-values-from !go:GO_0000060)))
  )

(define-ontology individual-hierarchy ()
  (class !go:term :partial)
  (object-property !go:go_isa :transitive)
  (individual-hierarchy !go:term !go:go_isa *small-piece-of-go*)
  )

(defun demonstrate-hierarchy ()
  "Print all sub(types|exists|individals) of !go:GO_0000060"
  (princ (abstract-syntax type-hierarchy))
  (sparql '(:select (?term) ()
	    (?term !rdfs:subClassOf !go:GO_0000060)
	    (:filter (and (not (equal ?term !owl:Nothing)) (not (equal ?term !go:GO_0000060)))))
	  :use-reasoner :jena
	  :kb (kb type-hierarchy)
	  :flatten t
	  :trace "Query the type hierarchy for all subclass of !go:GO_0000060")
  (princ (abstract-syntax existential-hierarchy))
  (sparql '(:select (?term) ()
	    (?term  !rdfs:subClassOf !go:probe)
	    (:filter (and (not (equal ?term !owl:Nothing))
		      (not (equal ?term !go:probe))))
	    )
	  :use-reasoner :jena
	  :kb (kb existential-hierarchy)
	  :flatten t
	  :trace "Query the existential hierarchy for all classes that are a subclass of the probe, defined as having some go:go_isa !go:GO_0000060")
  (format t "Can also call DIG-like query \"descendants\", instead of probe~%")
  (format t "(descendants (restriction !go:go_isa (some-values-from !go:GO_0000060)))~%")
  (format t "~{~a~%~}" (descendants (restriction !go:go_isa (some-values-from !go:GO_0000060)) (kb existential-hierarchy)))
  (sparql '(:select (?term) ()
	    (?term  !rdfs:subClassOf :_restriction)
	    (:_restriction !owl:onProperty !go:go_isa)
	    (:_restriction !owl:someValuesFrom !go:GO_0000060))
	  :use-reasoner :jena
	  :kb (kb existential-hierarchy)
	  :flatten t
	  :trace "Query the existential hierarchy for all classes that are expressed as restrictions go_isa go:GO_0000060")
  (princ (abstract-syntax individual-hierarchy))
  (sparql '(:select (?term) (:distinct t)
	    (?term !go:go_isa !go:GO_0000060)
	    )
	  :use-reasoner :jena
	  :kb (kb individual-hierarchy)
	  :flatten t
	  :trace "Query the individual hierarchy for all individual that are go_isa !go:GO_0000060"))