diff options
Diffstat (limited to 'lib/serializer.rb')
| -rw-r--r-- | lib/serializer.rb | 28 |
1 files changed, 18 insertions, 10 deletions
diff --git a/lib/serializer.rb b/lib/serializer.rb index e4cb541..62c1159 100644 --- a/lib/serializer.rb +++ b/lib/serializer.rb @@ -17,6 +17,7 @@ module OpenTox # 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.Model => { 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'] }] } , @@ -27,6 +28,8 @@ module OpenTox OT.Parameter => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , OT.Task => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , OTA.PatternMiningSupervised => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OTA.ClassificationLazySingleTarget => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , + OTA.RegressionLazySingleTarget => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , #classes for validation OT.Validation => { RDF["type"] => [{ "type" => "uri", "value" => OWL['Class'] }] } , @@ -45,6 +48,9 @@ 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 }] } , + OT.featureDataset => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.dependentVariables => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , + OT.paramValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , #object props for validation# OT.model => { RDF["type"] => [{ "type" => "uri", "value" => OWL.ObjectProperty }] } , @@ -103,6 +109,7 @@ module OpenTox 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.weightedAccuracy => { 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 }] } , @@ -126,7 +133,7 @@ module OpenTox 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 }] } , + #OT.paramValue => { RDF["type"] => [{ "type" => "uri", "value" => OWL.DatatypeProperty }] } , } @data_entries = {} @@ -157,23 +164,16 @@ module OpenTox # Add a dataset # @param [String] uri Dataset URI 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 a algorithm @@ -188,6 +188,13 @@ module OpenTox def add_model(uri,metadata) @object[uri] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Model }] } add_metadata uri, metadata + @object[metadata[OT.featureDataset]] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Dataset }] } + @object[metadata[OT.trainingDataset]] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Dataset }] } + @object[metadata[OT.dependentVariables]] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Feature }] } + # TODO: add algorithms from parameters + @object["http://ot-dev.in-silico.ch/algorithm/fminer/bbrc"] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] } + @object["http://ot-dev.in-silico.ch/algorithm/fminer/last"] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] } + @object["http://ot-dev.in-silico.ch/algorithm/lazar"] = { RDF["type"] => [{ "type" => "uri", "value" => OT.Algorithm }] } end # Add a task @@ -272,7 +279,7 @@ module OpenTox @object[genid][name] = [{"type" => type(entry), "value" => entry }] end end - elsif v.is_a? Array and u == RDF.type + elsif v.is_a? Array #and u == RDF.type @object[uri] = {} unless @object[uri] v.each do |value| @object[uri][u] = [] unless @object[uri][u] @@ -354,7 +361,8 @@ module OpenTox # @return [text/plain] Object OWL-DL in RDF/XML format 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` + # TODO: add base uri for ist services + `rapper -i ntriples -f 'xmlns:ot="#{OT.uri}"' -f 'xmlns:ota="#{OTA.uri}"' -f 'xmlns:dc="#{DC.uri}"' -f 'xmlns:rdf="#{RDF.uri}"' -f 'xmlns:owl="#{OWL.uri}"' -o rdfxml #{@path} 2>/dev/null` end # Convert to JSON as specified in http://n2.talis.com/wiki/RDF_JSON_Specification |