From 1daec5badcff31c591377017b32055aac775dbb7 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 4 Apr 2011 18:46:22 +0200
Subject: OT.isA substituted by RDF.type, identification of feature_types by
 RDF.type

---
 lib/model.rb | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

(limited to 'lib/model.rb')

diff --git a/lib/model.rb b/lib/model.rb
index 74408d8..422acd2 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -44,11 +44,10 @@ module OpenTox
         load_metadata(subjectid) if @metadata==nil or @metadata.size==0 or (@metadata.size==1 && @metadata.values[0]==@uri)
         algorithm = OpenTox::Algorithm::Generic.find(@metadata[OT.algorithm], subjectid)
         algorithm_title = algorithm ? algorithm.metadata[DC.title] : nil
-        algorithm_type = algorithm ? algorithm.metadata[OT.isA] : nil
+        algorithm_type = algorithm ? algorithm.metadata[RDF.type] : nil
         dependent_variable = OpenTox::Feature.find( @metadata[OT.dependentVariables],subjectid )
         dependent_variable_type = dependent_variable ? dependent_variable.feature_type : nil
-        type_indicators = [dependent_variable_type, @metadata[OT.isA], @metadata[DC.title], 
-          @uri, algorithm_type, algorithm_title] 
+        type_indicators = [dependent_variable_type, @metadata[RDF.type], @metadata[DC.title], @uri, algorithm_type, algorithm_title].flatten
         type_indicators.each do |type|
           case type
           when /(?i)classification/
@@ -187,7 +186,7 @@ module OpenTox
 
         if @neighbors.size == 0
           @prediction_dataset.add_feature(prediction_feature_uri, {
-            OT.isA => OT.MeasuredFeature,
+            RDF.type => [OT.MeasuredFeature],
             OT.hasSource => @uri,
             DC.creator => @uri,
             DC.title => URI.decode(File.basename( @metadata[OT.dependentVariables] )),
@@ -198,7 +197,7 @@ module OpenTox
 
         else
           @prediction_dataset.add_feature(prediction_feature_uri, {
-            OT.isA => OT.ModelPrediction,
+            RDF.type => [OT.ModelPrediction],
             OT.hasSource => @uri,
             DC.creator => @uri,
             DC.title => URI.decode(File.basename( @metadata[OT.dependentVariables] )),
@@ -215,7 +214,7 @@ module OpenTox
                 feature_uri = File.join( @prediction_dataset.uri, "feature", "descriptor", f.to_s)
                 features[feature] = feature_uri
                 @prediction_dataset.add_feature(feature_uri, {
-                  OT.isA => OT.Substructure,
+                  RDF.type => [OT.Substructure],
                   OT.smarts => feature,
                   OT.pValue => @p_values[feature],
                   OT.effect => @effects[feature]
@@ -236,7 +235,7 @@ module OpenTox
                 OT.compound => neighbor[:compound],
                 OT.similarity => neighbor[:similarity],
                 OT.measuredActivity => neighbor[:activity],
-                OT.isA => OT.Neighbor
+                RDF.type => [OT.Neighbor]
               })
               @prediction_dataset.add @compound.uri, neighbor_uri, true
               f = 0 unless f
@@ -250,7 +249,7 @@ module OpenTox
                 unless features.has_key? feature
                   features[feature] = feature_uri
                   @prediction_dataset.add_feature(feature_uri, {
-                    OT.isA => OT.Substructure,
+                    RDF.type => [OT.Substructure],
                     OT.smarts => feature,
                     OT.pValue => @p_values[feature],
                     OT.effect => @effects[feature]
-- 
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