(defvar *obo-noise-classes* 
  (list !obo:DbXref !obo:Definition !obo:ObsoleteClass !obo:Subset !obo:Synonym !obo:SynonymType))

(defmacro obo-standard-ont (abbrev)
  `'(:name ,abbrev :location ,(format nil "http://purl.org/obo/owl/~a"  abbrev)
     :dont-show ,*obo-noise-classes*
     ))

(defmacro an-ont (name location &rest keys)
  `'(:name ,name :location ,location ,@(mapcar 'eval keys)))

(defparameter *standard-ontologies*
  (list
   (obo-standard-ont :pato)
   (obo-standard-ont :caro)
   (obo-standard-ont :obo_rel)
   (obo-standard-ont :mp)
   (obo-standard-ont :mesh)
   (obo-standard-ont :mi)
   (obo-standard-ont :BP_XP_CL)
   (an-ont :bfo "http://www.ifomis.org/bfo/1.0")
   (an-ont :biopax "http://biopax.org/release/biopax-level2.owl")
   (an-ont :birnlex "http://www.nbirn.net/birnlex/1.2/BIRNLex-Main.owl")
   (an-ont :obi "file:///Users/alanr/repos/obi/trunk/src/ontology/branches/obil.owl"
	   :dont-show (list* !protegeowl:PAL-CONSTRAINT !protegeowl:DIRECTED-BINARY-RELATION *obo-noise-classes*)	   
	   :root !bfo:Entity)
   (an-ont :obid "file:///Users/alanr/repos/obi/trunk/src/ontology/branches/obid.owl"
	   :dont-show (list*  !protegeowl:PAL-CONSTRAINT !protegeowl:DIRECTED-BINARY-RELATION *obo-noise-classes*)
	   :root !bfo:Entity)
   (an-ont :obil "file:///Users/alanr/repos/obi/trunk/src/ontology/branches/obil.owl"
	   :dont-show (list* !protegeowl:PAL-CONSTRAINT !protegeowl:DIRECTED-BINARY-RELATION *obo-noise-classes*)	   
	   :root !bfo:Entity)
   (an-ont :obib "file:///Users/alanr/repos/obi/trunk/build/newids/obil.owl"
	   :dont-show (list* !protegeowl:PAL-CONSTRAINT !protegeowl:DIRECTED-BINARY-RELATION *obo-noise-classes*)	   
	   :root !bfo:Entity)
   (an-ont :birnorg "http://purl.org/nbirn/birnlex/ontology/BIRNLex-OrganismalTaxonomy.owl"
	   :dont-show (list*  !protegeowl:PAL-CONSTRAINT !protegeowl:DIRECTED-BINARY-RELATION *obo-noise-classes*))
   (an-ont :annot "http://sw.neurocommons.org/2007/annotations.owl")
   (an-ont :aba "http://sw.neurocommons.org/2007/aba.owl")
   (an-ont :family  "file:///Users/alanr/repos/pellet-1.4/test_data/misc/family.owl")
   (an-ont :owl11 "file:///Users/alanr/repos/pellet-1.4/test_data/misc/owl1.1.owl")
   (an-ont :swan "http://swan.mindinformatics.org/ontology/1.0/20070313/core.owl")
   (an-ont :biotop "http://biotop.googlecode.com/svn/trunk/biotop.owl")
   (an-ont :acgt "http://acgt.googlecode.com/svn/trunk/document.owl")
   (an-ont :bfo-ro "http://www.ifomis.uni-saarland.de/obo/ro/1.0/bfo/ro.owl")
   (an-ont :neurondb '("http://neuroweb.med.yale.edu/senselab/neuron_ontology.owl"
		       "http://neuroweb.med.yale.edu/senselab/neuron_ontology-bfo-mapping.owl" )
	   :dont-show '(list !obo:ObsoleteClass !obo:Definition !obo:ObsoleteProperty))
   (an-ont :annot1 "http://sw.neurocommons.org/2007/pubmed-annotations/00/7834200.rdf")
   (an-ont :brainpharm "http://neuroweb.med.yale.edu/senselab/brainpharm.owl")
   ))

(defun uri-of-standard-ontology (keyword)
  (getf (find keyword *standard-ontologies* :key 'second) :location))

(defun standard-ontology-classtree-options (keyword)
  (cddddr (find keyword *standard-ontologies* :key 'second)))

;  (let ((dont (getf (find keyword *standard-ontologies* :key 'second) :dont-show)))
;    (and dont (list :dont-show dont))))

(defun whichonts ()
  (let ((*print-case* :downcase))
  (loop for spec in *standard-ontologies*
       do (format t "~s ~s~%" (getf spec :name) (getf spec :location)))))