diff options
Diffstat (limited to 'lib/serializer.rb')
| -rw-r--r-- | lib/serializer.rb | 124 |
1 files changed, 124 insertions, 0 deletions
diff --git a/lib/serializer.rb b/lib/serializer.rb index 495702a..03c2639 100644 --- a/lib/serializer.rb +++ b/lib/serializer.rb @@ -26,6 +26,15 @@ module OpenTox 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.compound => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , OT.feature => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , @@ -34,6 +43,22 @@ module OpenTox 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 }] } , @@ -47,6 +72,47 @@ module OpenTox 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.hasSource => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } , OT.value => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } , @@ -121,6 +187,64 @@ module OpenTox @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Task }] } add_metadata uri, metadata end + + # Add a resource defined by resource_class and content + # (see documentation of add_content for example) + # @param [String] uri of resource + # @param [String] resource class, e.g. OT.Validation + # @param [Hash] content as hash + def add_resource(uri, resource_class, content) + @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => resource_class }] } + @@content_id = 1 + add_content uri, content + end + + private + @@content_id = 1 + + # Recursiv function to add content + # @example + # { DC.description => "bla", + # OT.similar_resources => [ "http://uri1", "http://uri2" ], + # OT.matrixCells => + # [ { RDF.type => OT.MatrixCell, OT.cellIndex=1 OT.cellValue => "xy" }, + # { RDF.type => OT.MatrixCell, OT.cellIndex=2 OT.cellValue => "z" } ], + # OT.info => { RDF.type => OT.ImportantInfo, + # DC.description => "blub" } + # } + # @param [String] uri + # @param [Hash] content as hash, uri must already have been added to @object + def add_content(uri, hash) + raise "content is no hash: "+hash.class.to_s unless hash.is_a?(Hash) + hash.each do |u,v| + if v.is_a? Hash + # value is again a hash, i.e. a new owl class is added + # first make sure type (==class) is set + type = v[RDF.type] + raise "type missing for "+u.to_s+" content:\n"+v.inspect unless type + raise "class unknown "+type.to_s+" (for "+u.to_s+")" unless @object.has_key?(type) + # create new node and add to current uri + genid = "_:#{type.split('#')[-1]}#{@@content_id}" + @@content_id += 1 + @object[uri] = {} unless @object[uri] + @object[uri][u] = [{ "type" => "bnode", "value" => genid }] + # add content to new class + add_hash(genid,v) + elsif v.is_a? Array + # value is an array, i.e. a list of values with property is added + v.each{ |vv| add_hash( uri, { u => vv } ) } + else # v.is_a? String + # simple string value + @object[uri] = {} unless @object[uri] + @object[uri][u] = [] unless @object[uri][u] + raise "property unknown "+u.to_s if !@object.has_key?(u) and u!=RDF.type + # use << to allow different values for one property + @object[uri][u] << {"type" => type(v), "value" => v } + end + end + end + + public # Add metadata # @param [Hash] metadata |