(define-ontology alzantibodies  (:base "http://www.w3.org/2001/sw/hcls/ontologies/reagent.owl"
				     :includes '(reagent))
  (let ((individuals nil)
	(count 0))
    (block limit
      (foreach-antibody-entry 
       (lambda(entry)
	 (flet ((field (field) 
		  (let ((value (cdr (assoc field entry))))
		    (if (and (char= (char value 0) #\")
			     (char= (char value (1- (length value))) #\"))
			(setq value (subseq value 1 (- (length value) 2))))
		    (if (or (equal value "NULL") (equal value " "))
			nil
			(progn
			  (#"replaceAll" (#"replaceAll" value "&" "&") "\"" "%22"))))))
;	   (when (> (incf count)  2000)
;	     (return-from limit nil))
	   (let* ((name (make-uri-base-relative (format nil "antibody-~a"  (field :antibodyid)) "alz:"))
		  (individual 
		   (individual name 
			       (annotation !alz:hasAntibodyId (field :antibodyid))
			       (and (field :epitope)
				    (annotation !hasEpitopeDescription (field :epitope)))
			       (and (field :specificity)
				    (annotation !hasSpecificityDescription  (field :specificity)))
			       (annotation !hasHostDescription 
					   (format nil "~a~a" 
						   (field :hostfastoutput) 
						   (if (field :hostExtraInfo)
						       (format nil " (~a)" (field :hostExtraInfo))
						       "")))
			       (annotation !hasReactivityDescription
					   (format nil "~a~a" 
						   (field :reactivityfastoutput) 
						   (if (field :reactivityextrainfo)
						       (format nil " (~a)" (field :reactivityextrainfo))
						       "")))
			       (annotation !hasCompanyDescription  (field :companyname))
			       (annotation !alz:hasAntigenClass (field :antigenId))
			       (type !Antibody))))
	     (push individual individuals))))))
    individuals))