Class: OpenTox::Serializer::Owl

Inherits:
Object
  • Object
show all
Defined in:
lib/serializer.rb

Overview

OWL-DL Serializer, modelled according to to n2.talis.com/wiki/RDF_JSON_Specification

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Owl

Returns a new instance of Owl.



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# File 'lib/serializer.rb', line 14

def initialize

  @object = {
    # this should come from opentox.owl
    OT.Compound => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.Feature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.NominalFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.NumericFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.StringFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.Dataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.DataEntry => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.FeatureValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.Algorithm => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.Parameter => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.Task => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    #classes for validation
    OT.Validation => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.ClassificationStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.ConfusionMatrix => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.ConfusionMatrixCell => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.ClassValueStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.RegressionStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.Crossvalidation => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.CrossvalidationInfo => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,
    OT.ErrorReport => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } ,

    OT.compound => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.feature => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.dataEntry => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.acceptValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.values => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.algorithm => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.parameters => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    #object props for validation#           
    OT.model => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.trainingDataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.predictionFeature => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.predictionDataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.crossvalidation => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.testTargetDataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.testDataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.classificationStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.confusionMatrix => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.confusionMatrixCell => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.classValueStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.regressionStatistics => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.validation => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.crossvalidationInfo => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,
    OT.dataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } ,

    DC.title => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    DC.identifier => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    DC.contributor => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    DC.creator => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    DC.description => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    DC.date => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.isA => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.Warnings => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    XSD.anyURI => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.hasStatus => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.resultURI => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.percentageCompleted => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    # annotation props for validation        
    OT.numUnpredicted => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.crossvalidationFold => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.numInstances => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.numWithoutClass => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.percentWithoutClass => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.percentUnpredicted => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.confusionMatrixActual => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.confusionMatrixPredicted => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.confusionMatrixValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.numIncorrect => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.percentCorrect => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.numCorrect => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.accuracy => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.trueNegativeRate => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.truePositiveRate => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.falseNegativeRate => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.falsePositiveRate => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.numTrueNegatives => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.numTruePositives => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.numFalseNegatives => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.numFalsePositives => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.classValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.precision => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.areaUnderRoc => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.weightedAreaUnderRoc => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.fMeasure => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.percentIncorrect => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.validationType => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.realRuntime => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.sampleCorrelationCoefficient => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.targetVarianceActual => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.targetVariancePredicted => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.meanAbsoluteError => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.sumSquaredError => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.rootMeanSquaredError => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.rSquare => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.stratified => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.numFolds => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.randomSeed => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.reportType => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.message => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.statusCode => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.actor => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,
    OT.errorCode => { RDF["type"] => [{ "type" => "uri", "value" => OWL.AnnotationProperty }] } ,

    OT.hasSource => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
    OT.value => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
    OT.paramScope => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
    OT.paramValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } ,
  }

  @data_entries = {}
  @values_id = 0
  @parameter_id = 0
  
  @classes = Set.new 
  @object_properties = Set.new
  @annotation_properties = Set.new
  @datatype_properties = Set.new

  @objects = Set.new
end

Instance Attribute Details

#object ⇒ Object

Returns the value of attribute object.



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# File 'lib/serializer.rb', line 12

def object
  @object
end

Instance Method Details

#add_algorithm(uri, metadata) ⇒ Object

Add a algorithm

Parameters:

  • uri (String) —

    Algorithm URI



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# File 'lib/serializer.rb', line 177

def add_algorithm(uri,metadata)
  @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] }
  add_metadata uri, metadata
end

#add_compound(uri) ⇒ Object

Add a compound

Parameters:

  • uri (String) —

    Compound URI



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# File 'lib/serializer.rb', line 142

def add_compound(uri)
  @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Compound }] }
end

#add_data_entry(compound, feature, value) ⇒ Object

Add a data entry

Parameters:

  • compound (String) —

    Compound URI

  • feature (String) —

    Feature URI

  • value (Boolead, Float) —

    Feature value



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# File 'lib/serializer.rb', line 281

def add_data_entry(compound,feature,value)
  add_compound(compound) unless @object[compound]
  add_feature(feature,{}) unless @object[feature]
  unless data_entry = @data_entries[compound]
    data_entry = "_:dataentry#{@data_entries.size}"
    @data_entries[compound] = data_entry
    @object[@dataset][OT.dataEntry] = [] unless @object[@dataset][OT.dataEntry]
    @object[@dataset][OT.dataEntry] << {"type" => "bnode", "value" => data_entry}
    @object[data_entry] = {
      RDF["type"] => [{ "type" => "uri", "value" => OT.DataEntry }],
      OT.compound => [{ "type" => "uri", "value" => compound }],
      OT.values => [],
    }
  end
  values = "_:values#{@values_id}"
  @values_id += 1
  @object[data_entry][OT.values] << {"type" => "bnode", "value" => values}
  case type(value)
  when "uri"
    v = [{ "type" => "uri", "value" => value}]
  when "literal"
    v = [{ "type" => "literal", "value" => value, "datatype" => datatype(value) }]
  else 
    raise "Illegal type #{type(value)} for #{value}."
  end
  @object[values] = {
    RDF["type"] => [{ "type" => "uri", "value" => OT.FeatureValue }],
    OT.feature => [{ "type" => "uri", "value" => feature }],
    OT.value => v
  }
  @object[feature][RDF["type"]] << { "type" => "uri", "value" => featuretype(value) }
end

#add_dataset(dataset) ⇒ Object

Add a dataset

Parameters:

  • uri (String) —

    Dataset URI



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# File 'lib/serializer.rb', line 155

def add_dataset(dataset)

  @dataset = dataset.uri

  @object[dataset.uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Dataset }] }

  add_metadata dataset.uri, dataset.metadata

  dataset.compounds.each { |compound| add_compound compound }
  
  dataset.features.each { |feature,metadata| add_feature feature,metadata }
  
  dataset.data_entries.each do |compound,entry|
    entry.each do |feature,values|
      values.each { |value| add_data_entry compound,feature,value }
    end
  end

end

#add_feature(uri, metadata) ⇒ Object

Add a feature

Parameters:

  • uri (String) —

    Feature URI



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# File 'lib/serializer.rb', line 148

def add_feature(uri,metadata)
  @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Feature }] }
  add_metadata uri, metadata
end

#add_metadata(uri, metadata) ⇒ Object

Add metadata

Parameters:

  • metadata (Hash) 


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# File 'lib/serializer.rb', line 256

def add_metadata(uri,metadata)
  id = 0
  metadata.each do |u,v|
    if v.is_a? Array and u == OT.parameters
      @object[uri][u] = [] unless @object[uri][u]
      v.each do |value|
        id+=1
        genid = "_:genid#{id}"
        @object[uri][u] << {"type" => "bnode", "value" => genid}
        @object[genid] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Parameter}] }
        value.each do |name,entry|
          @object[genid][name] = [{"type" => type(entry), "value" => entry }]
        end
      end
    else # v.is_a? String
      @object[uri] = {} unless @object[uri]
      @object[uri][u] = [{"type" => type(v), "value" => v }]
    end
  end
end

#add_model(uri, metadata) ⇒ Object

Add a model

Parameters:



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# File 'lib/serializer.rb', line 184

def add_model(uri,metadata)
  @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Model }] }
  add_metadata uri, metadata
end

#add_resource(uri, resource_class, content) ⇒ Object

Add a resource defined by resource_class and content (see documentation of add_content for example)

Parameters:

  • uri (String) —

    of resource

  • resource (String) —

    class, e.g. OT.Validation

  • content (Hash) —

    as hash



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# File 'lib/serializer.rb', line 201

def add_resource(uri, resource_class, content)
  @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => resource_class }] }
  @@content_id = 1
  add_content uri, content
end

#add_task(uri, metadata) ⇒ Object

Add a task

Parameters:



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# File 'lib/serializer.rb', line 191

def add_task(uri,metadata)
  @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Task }] }
  add_metadata uri, metadata
end

#to_json ⇒ text/plain

Convert to JSON as specified in n2.talis.com/wiki/RDF_JSON_Specification (Ambit services use a different JSON representation)

Returns:

  • (text/plain) —

    Object OWL-DL in JSON format



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# File 'lib/serializer.rb', line 351

def to_json
  #rdf_types
  Yajl::Encoder.encode(@object)
end

#to_ntriples ⇒ text/plain

Convert to N-Triples

Returns:

  • (text/plain) —

    Object OWL-DL in N-Triples format



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# File 'lib/serializer.rb', line 318

def to_ntriples

  @triples = Set.new
  @object.each do |s,entry|
    s = url(s) if type(s) == "uri"
    entry.each do |p,objects|
      p = url(p)
      objects.each do |o|
        case o["type"] 
        when "uri"
          o = url(o["value"])
        when "literal"
          o = literal(o["value"],datatype(o["value"]))
        when "bnode"
          o = o["value"]
        end
        @triples << [s,p,o]
      end
    end
  end
  @triples.sort.collect{ |s| s.join(' ').concat(" .") }.join("\n")+"\n"
end

#to_rdfxml ⇒ text/plain

Convert to RDF/XML

Returns:

  • (text/plain) —

    Object OWL-DL in RDF/XML format



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# File 'lib/serializer.rb', line 343

def to_rdfxml
  Tempfile.open("owl-serializer"){|f| f.write(self.to_ntriples); @path = f.path}
  `rapper -i ntriples -f 'xmlns:ot="#{OT.uri}"' -f 'xmlns:dc="#{DC.uri}"' -f 'xmlns:rdf="#{RDF.uri}"' -f 'xmlns:owl="#{OWL.uri}"' -o rdfxml #{@path} 2>/dev/null`
end