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module OpenTox
module Owl
attr_reader :uri, :model
def initialize
@model = Redland::Model.new Redland::MemoryStore.new
@parser = Redland::Parser.new
@serializer = Redland::Serializer.ntriples
# explicit typing
# this should come from http://opentox.org/data/documents/development/RDF%20files/OpenToxOntology/at_download/file (does not pass OWL-DL validation)
@model.add @uri, RDF['type'], OWL['Ontology']
# annotation properties
@model.add DC['source'], RDF['type'], OWL["AnnotationProperty"]
@model.add DC['identifier'], RDF['type'], OWL["AnnotationProperty"]
@model.add DC['title'], RDF['type'], OWL["AnnotationProperty"]
# object properties
@model.add OT['feature'], RDF['type'], OWL["ObjectProperty"]
@model.add OT['compound'], RDF['type'], OWL["ObjectProperty"]
@model.add OT['values'], RDF['type'], OWL["ObjectProperty"]
@model.add OT['tuple'], RDF['type'], OWL["ObjectProperty"] # added by ch
@model.add OT['parameters'], RDF['type'], OWL["ObjectProperty"]
# datatype properties
@model.add OT['value'], RDF['type'], OWL["DatatypeProperty"]
@model.add OT['paramValue'], RDF['type'], OWL["DatatypeProperty"]
@model.add OT['paramScope'], RDF['type'], OWL["DatatypeProperty"]
@model.add OT['hasSource'], RDF['type'], OWL["DatatypeProperty"]
# classes
@model.add OT['Dataset'], RDF['type'], OWL["Class"]
@model.add OT['FeatureValue'], RDF['type'], OWL["Class"]
@model.add OT['Tuple'], RDF['type'], OWL["Class"] # added by ch
@model.add OT['Feature'], RDF['type'], OWL["Class"]
@model.add OT['Compound'], RDF['type'], OWL["Class"]
@model.add OT['DataEntry'], RDF['type'], OWL["Class"]
@model.add OT['Parameter'], RDF['type'], OWL["Class"]
@model.add OT['Algorithm'], RDF['type'], OWL["Class"]
end
def owl_class
self.class.to_s.sub(/^OpenTox::/,'')
#@model.subject RDF['type'], OT[self.class.to_s.sub(/^OpenTox::/,'')]
end
def read(uri)
@parser.parse_into_model(@model,uri)
@uri = uri
end
def rdf=(rdf)
@uri = '/' unless @uri
@parser.parse_string_into_model(@model,rdf,@uri)
end
def rdf
@model.to_string
end
def uri=(uri)
identifier = uri
end
def to_ntriples
@serializer.model_to_string(Redland::Uri.new(@uri), @model)
end
def title
puts OT[self.owl_class]
@model.object(OT[self.owl_class], DC['title']).to_s
end
def parameters=(params)
params.each do |name, settings|
parameter = @model.create_resource
@model.add parameter, RDF['type'], OT['Parameter']
@model.add parameter, DC['title'], name
@model.add parameter, OT['paramScope'], settings[:scope]
@model.add parameter, OT['paramValue'], settings[:value]
end
end
def create_owl_statement(name,value)
r = @model.create_resource
@model.add r, RDF['type'], DC[name.gsub(/^[a-z]/) { |a| a.upcase }] # capitalize only the first letter
@model.add r, DC[name], value
end
def method_missing(name, *args)
# create magic setter methods
if /=/ =~ name.to_s
puts "create_owl_statement #{name.to_s.sub(/=/,'')}, #{args.first}"
create_owl_statement name.to_s.sub(/=/,''), args.first
else
raise "No method #{name}"
end
end
end
end
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