biointerchange 0.1.3 → 0.2.0

data/lib/biointerchange/genomics/gff3_reader.rb

@@ -1,31 +1,46 @@
+require 'stringio'
+
 module BioInterchange::Genomics
 
 class GFF3Reader
 
   # Creates a new instance of a Generic Feature Format Version 3 (GFF3) reader.
   #
+  # The reader supports batch processing.
+  #
   # +name+:: Optional name of the person who generated the GFF3 file.
   # +name_uri+:: Optional e-mail address of the person who generated the GFF3 file.
   # +date+:: Optional date of when the GFF3 file was produced.
-  def initialize(name = nil, name_uri = nil, date = nil)
+  # +batch_size+:: Optional integer that determines that number of features that
+  # should be processed in one go.
+  def initialize(name = nil, name_uri = nil, date = nil, batch_size = nil)
     @name = name
     @name_uri = name_uri
     @date = date
+    @batch_size = batch_size
   end 
 
   # Reads a GFF3 file from the input stream and returns an associated model.
   #
+  # If this method is called when +postponed?+ returns true, then the reading will
+  # continue from where it has been interrupted beforehand.
+  #
   # +inputstream+:: an instance of class IO or String that holds the contents of a GFF3 file
   def deserialize(inputstream)
     if inputstream.kind_of?(IO)
-      create_model(inputstream.read)
-    elsif inputstream.kind_of?(String) then
       create_model(inputstream)
+    elsif inputstream.kind_of?(String) then
+      create_model(StringIO.new(inputstream))
     else
       raise BioInterchange::Exceptions::ImplementationReaderError, 'The provided input stream needs to be either of type IO or String.'
     end
   end
 
+  # Returns true if the reading of the input was postponed due to a full batch.
+  def postponed?
+    @postponed
+  end
+
 protected
 
   def create_feature_set
@@ -33,32 +48,56 @@ protected
   end
 
   def create_model(gff3)
-    feature_set = create_feature_set
-    gff3.each_line { |line|
+    if @postponed then
+      @postponed = false
+      @feature_set.prune
+    else
+      @feature_set = create_feature_set
+    end
+    feature_no = 0
+
+    # Note: there is a `while true` statement at the end of this block!
+    begin
+      line = gff3.readline
+      line.chomp!
+
       next if line.start_with?('#') and not line.start_with?('##')
 
       # Ignore sequences for now.
       break if line.start_with?('##FASTA')
 
       unless line.start_with?('##') then
-        add_feature(feature_set, line)
+        add_feature(@feature_set, line)
+        feature_no += 1
+
+        if @batch_size and feature_no >= @batch_size then
+          @postponed = true
+          break
+        end
       else
-        add_pragma(feature_set, line)
+        add_pragma(@feature_set, line)
       end
-    }
+    rescue EOFError
+      # Expected. Do nothing, since just the end of the file/input has been reached.
+      break
+    end while true
 
-    feature_set
+    @feature_set
   end
 
   def add_feature(feature_set, line)
     line.chomp!
     seqid, source, type, start_coordinate, end_coordinate, score, strand, phase, attributes = line.split("\t")
 
-    # The type might be a SO/SOFA term, SO/SOFA accession, or other term (it stays a string then):
-    if type.match(/SO:\d+/) then
-      type = RDF::URI.new("http://purl.obolibrary.org/obo/#{type.sub(':', '_')}")
-    elsif BioInterchange::SOFA.methods.include?(type.gsub(' ', '_').to_sym)
-      type = BioInterchange::SOFA.send(type.gsub(' ', '_'))
+    # The type might be a SO/SOFA term or SO/SOFA accession:
+    begin
+      if type.match(/^SO:\d{7}$/) then
+        type = RDF::URI.new("http://www.sequenceontology.org/miso/current_release/term/#{feature.type}")
+      else
+        type = BioInterchange::SOFA.send(BioInterchange.make_safe_label(type))
+      end
+    rescue NoMethodError
+      raise BioInterchange::Exceptions::InputFormatError, 'Type of feature is set to an unknown SOFA term.'
     end
 
     # String to numeric value conversions:
@@ -88,9 +127,7 @@ protected
       phase = nil
     end
 
-    temp = {}
-    attributes.split(';').map { |assignment| match = assignment.match(/([^=]+)=(.+)/) ; { match[1].strip => match[2].split(',').map { |value| value.strip } } }.map { |hash| hash.each_pair { |tag,list| temp[tag] = list } }
-    attributes = temp
+    attributes = split_attributes(attributes)
 
     feature_set.add(BioInterchange::Genomics::GFF3Feature.new(seqid, source, type, start_coordinate, end_coordinate, score, strand, phase, attributes))
   end
@@ -100,20 +137,41 @@ protected
     name, value = line[2..-1].split(/\s/, 2)
     value.strip!
     
-    # Interpret pragmas depending on their definition:
-    if name == 'gff-version' then
+    # Interpret pragmas depending on their definition (sorted alphabetically):
+    if name == 'feature-ontology' then
+      ontologies = feature_set.pragma(name)
+      ontologies = { name => [] } unless ontologies
+      ontologies[name] << value
+      feature_set.set_pragma(name, ontologies)
+    elsif name == 'genome-build' then
+      builds = feature_set.pragma(name)
+      builds = { name => {} } unless builds
+      source, build_name = value.split(/\s+/, 2)
+      build_name.sub!(/\s.*$/, '') # Remove possible comments
+      builds[name][source] = build_name
+      feature_set.set_pragma(name, builds)
+    elsif name == 'gff-version' then
       feature_set.set_pragma(name, { name => value.to_f })
     elsif name == 'sequence-region' then
       regions = feature_set.pragma(name)
       regions = {} unless regions
       seqid, start_coordinate, end_coordinate = value.split(/\s+/, 3)
-      regions[seqid] = BioInterchange::Genomics::GFF3NamedRegion.new(seqid, start_coordinate.to_i, end_coordinate.to_i)
+      regions[seqid] = BioInterchange::Genomics::GFF3Landmark.new(seqid, start_coordinate.to_i, end_coordinate.to_i)
       feature_set.set_pragma(name, regions)
+    elsif name == 'species' then
+      feature_set.set_pragma(name, { name => value })
     else
       # Unhandled pragma. Just save the value in its string form.
       feature_set.set_pragma(name, value)
     end
   end
+
+  def split_attributes(attribute_string)
+    attributes = {}
+    attribute_string.split(';').map { |assignment| match = assignment.match(/([^=]+)=(.+)/) ; { match[1].strip => match[2].split(',').map { |value| value.strip } } }.map { |hash| hash.each_pair { |tag,list| attributes[tag] = list } }
+    attributes
+  end
+
 end
 
 end

data/lib/biointerchange/genomics/gvf_reader.rb

@@ -7,7 +7,7 @@ class GVFReader < GFF3Reader
   # +name+:: Optional name of the person who generated the GVF file.
   # +name_uri+:: Optional e-mail address of the person who generated the GVF file.
   # +date+:: Optional date of when the GVF file was produced.
-  def initialize(name = nil, name_uri = nil, date = nil)
+  def initialize(name = nil, name_uri = nil, date = nil, batch_size = nil)
     # Remember: calling super without brackets passes all arguments of initialize!
     super
   end
@@ -23,8 +23,14 @@ protected
     name, value = line[2..-1].split(/\s/, 2)
     value.strip!
 
-    # Interpret pragmas, and if not known, delegate to GFF3Reader:
-    if name == 'gvf-version' then
+    # Interpret pragmas, and if not known, delegate to GFF3Reader (in alphabetical order):
+    if name == 'attribute-method' or name == 'data-source' or name == 'score-method' or name == 'source-method' or name == 'technology-platform' then
+      attributes = split_attributes(value)
+      structured_attributes = feature_set.pragma(name)
+      structured_attributes = { name => [] } unless structured_attributes
+      structured_attributes[name] << attributes
+      feature_set.set_pragma(name, structured_attributes)
+    elsif name == 'gvf-version' then
       feature_set.set_pragma(name, { name => value.to_f })
     else
       super(feature_set, line)

data/lib/biointerchange/gff3o.rb

@@ -3,6 +3,18 @@ module BioInterchange
 
 class GFF3O
 
+  # Establishes the landmark (e.g. a chromosome) on which a feature is located.
+  # (http://www.biointerchange.org/gff3o#GFF3_0004)
+  def self.seqid
+    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0004')
+  end
+
+  # Type of the feature, which is either an entry the "lite" version of the Sequence Ontology (SOFA) or a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).
+  # (http://www.biointerchange.org/gff3o#GFF3_0006)
+  def self.type
+    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006')
+  end
+
   # Either:
   #   Strand of the feature.
   #   (http://www.biointerchange.org/gff3o#GFF3_0010)
@@ -101,10 +113,10 @@ class GFF3O
     return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0047')
   end
 
-  # ID of the landmark that establishes the coordinate system for the current feature.
-  # (http://www.biointerchange.org/gff3o#GFF3_0004)
-  def self.seqid
-    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0004')
+  # Explicit link-out to one or more ontologies that have been used for describing features. This is a meta comment about the URIs that link out to SO/SOFA or other ontologies.
+  # (http://www.biointerchange.org/gff3o#GFF3_0056)
+  def self.feature_ontology
+    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0056')
   end
 
   # A free text qualifier that describes the algorithm or operating procedure that generated this feature.  For example, the name of the software that generated this feature or a database name.
@@ -113,20 +125,17 @@ class GFF3O
     return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0005')
   end
 
-  # Type of the feature, which is either a term from the "lite" version of the Sequence Ontology (SOFA), a term from the full Sequence Ontology (SO) that is a child of sequence_feature (SO:0000110), or a SOFA or SO accession number.
-  # (http://www.biointerchange.org/gff3o#GFF3_0006)
-  def self.type
-    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006')
-  end
-
   # Either:
   #   Start coordinate of the feature on the seqid landmark.
   #   (http://www.biointerchange.org/gff3o#GFF3_0007)
   # Or:
   #   Start coordinate of the target.
   #   (http://www.biointerchange.org/gff3o#GFF3_0042)
+  # Or:
+  #   Genomic start coordinate of the landmark.
+  #   (http://www.biointerchange.org/gff3o#GFF3_0054)
   def self.start
-    return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0007'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0042') ]
+    return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0007'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0042'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0054') ]
   end
 
   # Either:
@@ -135,8 +144,11 @@ class GFF3O
   # Or:
   #   End coordinate of the target.
   #   (http://www.biointerchange.org/gff3o#GFF3_0043)
+  # Or:
+  #   Genomic end coordinate of the landmark.
+  #   (http://www.biointerchange.org/gff3o#GFF3_0055)
   def self.end
-    return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0008'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0043') ]
+    return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0008'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0043'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0055') ]
   end
 
   # Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features.
@@ -175,26 +187,10 @@ class GFF3O
     return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0029')
   end
 
-  # Properties that are directly associated with DBXRef class instances.
-  # (http://www.biointerchange.org/gff3o#GFF3_0031)
-  def self.dbxref_properties
-    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0031')
-  end
-
-  # Either:
-  #   Name of an external database. For example, "dbSNP" or "OMIM".
-  #   (http://www.biointerchange.org/gff3o#GFF3_0032)
-  # Or:
-  #   Name of a feature, which can be used for display purposes. The name is not a unique property among features.
-  #   (http://www.biointerchange.org/gff3o#GFF3_0036)
+  # Name of a feature, which can be used for display purposes. The name is not a unique property among features.
+  # (http://www.biointerchange.org/gff3o#GFF3_0036)
   def self.name
-    return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0032'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0036') ]
-  end
-
-  # External database identifier. For example, for dbSNP, this identifier could be "rs3131969".
-  # (http://www.biointerchange.org/gff3o#GFF3_0033)
-  def self.xref
-    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0033')
+    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0036')
   end
 
   # An alternative name for a feature. This can be another descriptive name of a feature, such as a locus name or accession number.
@@ -227,6 +223,18 @@ class GFF3O
     return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0049')
   end
 
+  # Properties that are directly associated with Landmark class instances.
+  # (http://www.biointerchange.org/gff3o#GFF3_0052)
+  def self.landmark_properties
+    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0052')
+  end
+
+  # ID that uniquely establishes the Landmark's identity within a Set.
+  # (http://www.biointerchange.org/gff3o#GFF3_0053)
+  def self.id
+    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0053')
+  end
+
   # Set of genomic sequence features, whose identifiers are unique within the set.
   # (http://www.biointerchange.org/gff3o#GFF3_0001)
   def self.Set
@@ -251,18 +259,18 @@ class GFF3O
     return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0016')
   end
 
-  # A class describing relationships between features and external databases.
-  # (http://www.biointerchange.org/gff3o#GFF3_0030)
-  def self.DBXRef
-    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0030')
-  end
-
   # Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment.
   # (http://www.biointerchange.org/gff3o#GFF3_0038)
   def self.Target
     return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0038')
   end
 
+  # A landmark that establishes the coordinate system for features.
+  # (http://www.biointerchange.org/gff3o#GFF3_0051)
+  def self.Landmark
+    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0051')
+  end
+
   # Location on the positive (forward) strand.
   # (http://www.biointerchange.org/gff3o#GFF3_0017)
   def self.Positive
@@ -291,6 +299,12 @@ class GFF3O
   #
   # +uri+:: URI that is tested for being an object property
   def self.is_object_property?(uri)
+    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0004') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006') then
+      return true
+    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0010') then
       return true
     end
@@ -336,6 +350,9 @@ class GFF3O
     if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0050') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0056') then
+      return true
+    end
     return false
   end
 
@@ -343,15 +360,9 @@ class GFF3O
   #
   # +uri+:: URI that is tested for being a datatype property
   def self.is_datatype_property?(uri)
-    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0004') then
-      return true
-    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0005') then
       return true
     end
-    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006') then
-      return true
-    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0007') then
       return true
     end
@@ -382,15 +393,6 @@ class GFF3O
     if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0029') then
       return true
     end
-    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0031') then
-      return true
-    end
-    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0032') then
-      return true
-    end
-    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0033') then
-      return true
-    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0036') then
       return true
     end
@@ -418,6 +420,18 @@ class GFF3O
     if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0049') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0052') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0053') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0054') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0055') then
+      return true
+    end
     return false
   end
 
@@ -437,10 +451,10 @@ class GFF3O
     if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0016') then
       return true
     end
-    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0030') then
+    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0038') then
       return true
     end
-    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0038') then
+    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0051') then
       return true
     end
     return false
@@ -488,7 +502,7 @@ class GFF3O
   end
 
 private
-  @@parent_properties = { RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0010') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0012') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0014') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0015') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0025') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0021') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0023') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0025') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0034') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0039') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0045') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0044') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0047') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0050') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0044') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0004') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0005') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0007') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0008') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0009') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0011') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0013') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0029') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0022') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0027') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0024') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0027') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0032') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0031') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0033') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0031') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0036') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0037') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0041') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0040') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0042') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0040') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0043') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0040') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0046') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0048') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0049') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') }
+  @@parent_properties = { RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0004') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0006') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0010') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0012') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0014') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0015') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0025') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0021') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0023') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0025') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0034') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0039') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0045') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0044') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0047') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0050') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0044') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0056') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0025') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0005') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0007') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0008') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0009') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0011') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0013') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0029') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0022') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0027') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0024') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0027') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0036') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0037') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0041') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0040') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0042') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0040') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0043') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0040') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0046') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0048') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0049') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0053') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0052') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0054') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0052') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0055') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0052') }
 
 end
 

data/lib/biointerchange/goxref.rb

@@ -0,0 +1,867 @@
+module BioInterchange
+
+class GOXRef
+
+  # Returns the link-out URI for objects of "Arabidopsis Genome Initiative".
+  def self.AGI_LocusCode
+    RDF::URI.new("http://arabidopsis.org/servlets/TairObject?type=locus&name=")
+  end
+
+  # Returns the link-out URI for objects of "PlasmoDB Plasmodium Genome Resource".
+  def self.ApiDB_PlasmoDB
+    RDF::URI.new("http://www.plasmodb.org/gene/")
+  end
+
+  # Returns the link-out URI for objects of "AraCyc metabolic pathway database for Arabidopsis thaliana".
+  def self.AraCyc
+    RDF::URI.new("http://www.arabidopsis.org:1555/ARA/NEW-IMAGE?type=NIL&object=")
+  end
+
+  # Returns the link-out URI for objects of "A Systematic Annotation Package for Community Analysis of Genomes".
+  def self.ASAP
+    RDF::URI.new("https://asap.ahabs.wisc.edu/annotation/php/feature_info.php?FeatureID=")
+  end
+
+  # Returns the link-out URI for objects of "Aspergillus Genome Database".
+  def self.AspGD
+    RDF::URI.new("http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid=")
+  end
+
+  # Returns the link-out URI for objects of "Aspergillus Genome Database".
+  def self.AspGD_LOCUS
+    RDF::URI.new("http://www.aspergillusgenome.org/cgi-bin/locus.pl?locus=")
+  end
+
+  # Returns the link-out URI for objects of "Aspergillus Genome Database".
+  def self.AspGD_REF
+    RDF::URI.new("http://www.aspergillusgenome.org/cgi-bin/reference/reference.pl?dbid=")
+  end
+
+  # Returns the link-out URI for objects of "Basic Formal Ontology".
+  def self.BFO
+    RDF::URI.new("http://purl.obolibrary.org/obo/BFO_")
+  end
+
+  # Returns the link-out URI for objects of "BioCyc collection of metabolic pathway databases".
+  def self.BioCyc
+    RDF::URI.new("http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=")
+  end
+
+  # Returns the link-out URI for objects of "BioModels Database".
+  def self.BIOMD
+    RDF::URI.new("http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid=")
+  end
+
+  # Returns the link-out URI for objects of "BRENDA, The Comprehensive Enzyme Information System".
+  def self.BRENDA
+    RDF::URI.new("http://www.brenda-enzymes.info/php/result_flat.php4?ecno=")
+  end
+
+  # Returns the link-out URI for objects of "Magnaporthe grisea Database".
+  def self.Broad_MGG
+    RDF::URI.new("http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/GeneLocus.html?sp=S")
+  end
+
+  # Returns the link-out URI for objects of "Catalog of Fishes genus database".
+  def self.CASGEN
+    RDF::URI.new("http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Genus&id=")
+  end
+
+  # Returns the link-out URI for objects of "Catalog of Fishes publications database".
+  def self.CASREF
+    RDF::URI.new("http://research.calacademy.org/research/ichthyology/catalog/getref.asp?id=")
+  end
+
+  # Returns the link-out URI for objects of "Catalog of Fishes species database".
+  def self.CASSPC
+    RDF::URI.new("http://research.calacademy.org/research/ichthyology/catalog/getname.asp?rank=Species&id=1979")
+  end
+
+  # Returns the link-out URI for objects of "Conserved Domain Database at NCBI".
+  def self.CDD
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=")
+  end
+
+  # Returns the link-out URI for objects of "Candida Genome Database".
+  def self.CGD
+    RDF::URI.new("http://www.candidagenome.org/cgi-bin/locus.pl?dbid=")
+  end
+
+  # Returns the link-out URI for objects of "Candida Genome Database".
+  def self.CGD_LOCUS
+    RDF::URI.new("http://www.candidagenome.org/cgi-bin/locus.pl?locus=")
+  end
+
+  # Returns the link-out URI for objects of "Candida Genome Database".
+  def self.CGD_REF
+    RDF::URI.new("http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=")
+  end
+
+  # Returns the link-out URI for objects of "Chemical Entities of Biological Interest".
+  def self.CHEBI
+    RDF::URI.new("http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:")
+  end
+
+  # Returns the link-out URI for objects of "Cell Type Ontology".
+  def self.CL
+    RDF::URI.new("http://purl.obolibrary.org/obo/CL_")
+  end
+
+  # Returns the link-out URI for objects of "NCBI COG cluster".
+  def self.COG_Cluster
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=")
+  end
+
+  # Returns the link-out URI for objects of "NCBI COG function".
+  def self.COG_Function
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=")
+  end
+
+  # Returns the link-out URI for objects of "NCBI COG pathway".
+  def self.COG_Pathway
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=")
+  end
+
+  # Returns the link-out URI for objects of "CORUM - the Comprehensive Resource of Mammalian protein complexes".
+  def self.CORUM
+    RDF::URI.new("http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=")
+  end
+
+  # Returns the link-out URI for objects of "NCBI dbSNP".
+  def self.dbSNP
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=")
+  end
+
+  # Returns the link-out URI for objects of "DNA Databank of Japan".
+  def self.DDBJ
+    RDF::URI.new("http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=")
+  end
+
+  # Returns the link-out URI for objects of "dictyBase".
+  def self.dictyBase
+    RDF::URI.new("http://dictybase.org/gene/")
+  end
+
+  # Returns the link-out URI for objects of "dictyBase".
+  def self.dictyBase_gene_name
+    RDF::URI.new("http://dictybase.org/gene/")
+  end
+
+  # Returns the link-out URI for objects of "dictyBase literature references".
+  def self.dictyBase_REF
+    RDF::URI.new("http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=")
+  end
+
+  # Returns the link-out URI for objects of "Digital Object Identifier".
+  def self.DOI
+    RDF::URI.new("http://dx.doi.org/DOI:")
+  end
+
+  # Returns the link-out URI for objects of "Enzyme Commission".
+  def self.EC
+    RDF::URI.new("http://www.expasy.org/enzyme/")
+  end
+
+  # Returns the link-out URI for objects of "EchoBASE post-genomic database for Escherichia coli".
+  def self.EchoBASE
+    RDF::URI.new("http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=")
+  end
+
+  # Returns the link-out URI for objects of "EcoGene Database of Escherichia coli Sequence and Function".
+  def self.ECK
+    RDF::URI.new("http://www.ecogene.org/geneInfo.php?eck_id=")
+  end
+
+  # Returns the link-out URI for objects of "Encyclopedia of E. coli metabolism".
+  def self.EcoCyc
+    RDF::URI.new("http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=")
+  end
+
+  # Returns the link-out URI for objects of "Encyclopedia of E. coli metabolism".
+  def self.EcoCyc_REF
+    RDF::URI.new("http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=")
+  end
+
+  # Returns the link-out URI for objects of "EcoGene Database of Escherichia coli Sequence and Function".
+  def self.ECOGENE
+    RDF::URI.new("http://www.ecogene.org/geneInfo.php?eg_id=")
+  end
+
+  # Returns the link-out URI for objects of "EMBL Nucleotide Sequence Database".
+  def self.EMBL
+    RDF::URI.new("http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=")
+  end
+
+  # Returns the link-out URI for objects of "European Nucleotide Archive".
+  def self.ENA
+    RDF::URI.new("http://www.ebi.ac.uk/ena/data/view/")
+  end
+
+  # Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
+  def self.ENSEMBL
+    RDF::URI.new("http://www.ensembl.org/id/")
+  end
+
+  # Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
+  def self.ENSEMBL_GeneID
+    RDF::URI.new("http://www.ensembl.org/id/")
+  end
+
+  # Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
+  def self.ENSEMBL_ProteinID
+    RDF::URI.new("http://www.ensembl.org/id/")
+  end
+
+  # Returns the link-out URI for objects of "Ensembl database of automatically annotated genomic data".
+  def self.ENSEMBL_TranscriptID
+    RDF::URI.new("http://www.ensembl.org/id/")
+  end
+
+  # Returns the link-out URI for objects of "Swiss Institute of Bioinformatics enzyme database".
+  def self.ENZYME
+    RDF::URI.new("http://www.expasy.ch/cgi-bin/nicezyme.pl?")
+  end
+
+  # Returns the link-out URI for objects of "Drosophila gross anatomy".
+  def self.FBbt
+    RDF::URI.new("http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:")
+  end
+
+  # Returns the link-out URI for objects of "Human Genome Database".
+  def self.GDB
+    RDF::URI.new("http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:")
+  end
+
+  # Returns the link-out URI for objects of "GenBank".
+  def self.GenBank
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=")
+  end
+
+  # Returns the link-out URI for objects of "Domain Architecture Classification".
+  def self.Gene3D
+    RDF::URI.new("http://gene3d.biochem.ucl.ac.uk/superfamily/?accession=")
+  end
+
+  # Returns the link-out URI for objects of "Glossina morsitans GeneDB".
+  def self.GeneDB_Gmorsitans
+    RDF::URI.new("http://www.genedb.org/genedb/Search?organism=glossina&name=")
+  end
+
+  # Returns the link-out URI for objects of "Leishmania major GeneDB".
+  def self.GeneDB_Lmajor
+    RDF::URI.new("http://www.genedb.org/genedb/Search?organism=leish&name=")
+  end
+
+  # Returns the link-out URI for objects of "Plasmodium falciparum GeneDB".
+  def self.GeneDB_Pfalciparum
+    RDF::URI.new("http://www.genedb.org/genedb/Search?organism=malaria&name=")
+  end
+
+  # Returns the link-out URI for objects of "Schizosaccharomyces pombe GeneDB".
+  def self.GeneDB_Spombe
+    RDF::URI.new("http://old.genedb.org/genedb/Search?organism=pombe&name=")
+  end
+
+  # Returns the link-out URI for objects of "Trypanosoma brucei GeneDB".
+  def self.GeneDB_Tbrucei
+    RDF::URI.new("http://www.genedb.org/genedb/Search?organism=tryp&name=")
+  end
+
+  # Returns the link-out URI for objects of "NCBI Gene Expression Omnibus".
+  def self.GEO
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=")
+  end
+
+  # Returns the link-out URI for objects of "Gene Ontology Database".
+  def self.GO
+    RDF::URI.new("http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:")
+  end
+
+  # Returns the link-out URI for objects of "Gene Ontology Database references".
+  def self.GO_REF
+    RDF::URI.new("http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:")
+  end
+
+  # Returns the link-out URI for objects of "Gene Ontology Normal Usage Tracking System (GONUTS)".
+  def self.GONUTS
+    RDF::URI.new("http://gowiki.tamu.edu/wiki/index.php/")
+  end
+
+  # Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
+  def self.GR
+    RDF::URI.new("http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=")
+  end
+
+  # Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
+  def self.GR_GENE
+    RDF::URI.new("http://www.gramene.org/db/genes/search_gene?acc=")
+  end
+
+  # Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
+  def self.GR_PROTEIN
+    RDF::URI.new("http://www.gramene.org/db/protein/protein_search?acc=")
+  end
+
+  # Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
+  def self.GR_QTL
+    RDF::URI.new("http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=")
+  end
+
+  # Returns the link-out URI for objects of "Gramene: A Comparative Mapping Resource for Grains".
+  def self.GR_REF
+    RDF::URI.new("http://www.gramene.org/db/literature/pub_search?ref_id=")
+  end
+
+  # Returns the link-out URI for objects of "H-invitational Database".
+  def self.H_invDB_cDNA
+    RDF::URI.new("http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=")
+  end
+
+  # Returns the link-out URI for objects of "H-invitational Database".
+  def self.H_invDB_locus
+    RDF::URI.new("http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=")
+  end
+
+  # Returns the link-out URI for objects of "High-quality Automated and Manual Annotation of microbial Proteomes".
+  def self.HAMAP
+    RDF::URI.new("http://us.expasy.org/unirules/")
+  end
+
+  # Returns the link-out URI for objects of "HUGO Gene Nomenclature Committee".
+  def self.HGNC
+    RDF::URI.new("http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:")
+  end
+
+  # Returns the link-out URI for objects of "HUGO Gene Nomenclature Committee".
+  def self.HGNC_gene
+    RDF::URI.new("http://www.genenames.org/data/hgnc_data.php?app_sym=")
+  end
+
+  # Returns the link-out URI for objects of "Human Protein Atlas tissue profile information".
+  def self.HPA
+    RDF::URI.new("http://www.proteinatlas.org/tissue_profile.php?antibody_id=")
+  end
+
+  # Returns the link-out URI for objects of "Human Protein Atlas antibody information".
+  def self.HPA_antibody
+    RDF::URI.new("http://www.proteinatlas.org/antibody_info.php?antibody_id=")
+  end
+
+  # Returns the link-out URI for objects of "Integrated Microbial Genomes; JGI web site for genome annotation".
+  def self.IMG
+    RDF::URI.new("http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=")
+  end
+
+  # Returns the link-out URI for objects of "IntAct protein interaction database".
+  def self.IntAct
+    RDF::URI.new("http://www.ebi.ac.uk/intact/search/do/search?searchString=")
+  end
+
+  # Returns the link-out URI for objects of "InterPro database of protein domains and motifs".
+  def self.InterPro
+    RDF::URI.new("http://www.ebi.ac.uk/interpro/IEntry?ac=")
+  end
+
+  # Returns the link-out URI for objects of "International Standard Book Number".
+  def self.ISBN
+    RDF::URI.new("http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=")
+  end
+
+  # Returns the link-out URI for objects of "International Union of Pharmacology".
+  def self.IUPHAR_GPCR
+    RDF::URI.new("http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=")
+  end
+
+  # Returns the link-out URI for objects of "International Union of Pharmacology".
+  def self.IUPHAR_RECEPTOR
+    RDF::URI.new("http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=")
+  end
+
+  # Returns the link-out URI for objects of "Comprehensive Microbial Resource at the J. Craig Venter Institute".
+  def self.JCVI_CMR
+    RDF::URI.new("http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=")
+  end
+
+  # Returns the link-out URI for objects of "Comprehensive Microbial Resource at the J. Craig Venter Institute".
+  def self.JCVI_EGAD
+    RDF::URI.new("http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=")
+  end
+
+  # Returns the link-out URI for objects of "Genome Properties database at the J. Craig Venter Institute".
+  def self.JCVI_GenProp
+    RDF::URI.new("http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=")
+  end
+
+  # Returns the link-out URI for objects of "Medicago truncatula genome database at the J. Craig Venter Institute ".
+  def self.JCVI_Medtr
+    RDF::URI.new("http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=")
+  end
+
+  # Returns the link-out URI for objects of "TIGRFAMs HMM collection at the J. Craig Venter Institute".
+  def self.JCVI_TIGRFAMS
+    RDF::URI.new("http://search.jcvi.org/search?p&q=")
+  end
+
+  # Returns the link-out URI for objects of "Digital archive of scholarly articles".
+  def self.JSTOR
+    RDF::URI.new("http://www.jstor.org/stable/")
+  end
+
+  # Returns the link-out URI for objects of "KEGG Enzyme Database".
+  def self.KEGG_ENZYME
+    RDF::URI.new("http://www.genome.jp/dbget-bin/www_bget?ec:")
+  end
+
+  # Returns the link-out URI for objects of "KEGG LIGAND Database".
+  def self.KEGG_LIGAND
+    RDF::URI.new("http://www.genome.jp/dbget-bin/www_bget?cpd:")
+  end
+
+  # Returns the link-out URI for objects of "KEGG Pathways Database".
+  def self.KEGG_PATHWAY
+    RDF::URI.new("http://www.genome.jp/dbget-bin/www_bget?path:")
+  end
+
+  # Returns the link-out URI for objects of "KEGG Reaction Database".
+  def self.KEGG_REACTION
+    RDF::URI.new("http://www.genome.jp/dbget-bin/www_bget?rn:")
+  end
+
+  # Returns the link-out URI for objects of "LifeDB".
+  def self.LIFEdb
+    RDF::URI.new("http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=")
+  end
+
+  # Returns the link-out URI for objects of "Adult Mouse Anatomical Dictionary".
+  def self.MA
+    RDF::URI.new("http://www.informatics.jax.org/searches/AMA.cgi?id=MA:")
+  end
+
+  # Returns the link-out URI for objects of "MaizeGDB".
+  def self.MaizeGDB
+    RDF::URI.new("http://www.maizegdb.org/cgi-bin/id_search.cgi?id=")
+  end
+
+  # Returns the link-out URI for objects of "MaizeGDB".
+  def self.MaizeGDB_Locus
+    RDF::URI.new("http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=")
+  end
+
+  # Returns the link-out URI for objects of "MEROPS peptidase database".
+  def self.MEROPS
+    RDF::URI.new("http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=")
+  end
+
+  # Returns the link-out URI for objects of "MEROPS peptidase database".
+  def self.MEROPS_fam
+    RDF::URI.new("http://merops.sanger.ac.uk/cgi-bin/famsum?family=")
+  end
+
+  # Returns the link-out URI for objects of "Medical Subject Headings".
+  def self.MeSH
+    RDF::URI.new("http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=")
+  end
+
+  # Returns the link-out URI for objects of "Metabolic Encyclopedia of metabolic and other pathways".
+  def self.MetaCyc
+    RDF::URI.new("http://biocyc.org/META/NEW-IMAGE?type=NIL&object=")
+  end
+
+  # Returns the link-out URI for objects of "Mouse Genome Informatics".
+  def self.MGI
+    RDF::URI.new("http://www.informatics.jax.org/accession/")
+  end
+
+  # Returns the link-out URI for objects of "MIPS Functional Catalogue".
+  def self.MIPS_funcat
+    RDF::URI.new("http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=")
+  end
+
+  # Returns the link-out URI for objects of "MGED Ontology".
+  def self.MO
+    RDF::URI.new("http://mged.sourceforge.net/ontologies/MGEDontology.php#")
+  end
+
+  # Returns the link-out URI for objects of "ModBase comprehensive Database of Comparative Protein Structure Models".
+  def self.ModBase
+    RDF::URI.new("http://salilab.org/modbase/searchbyid?databaseID=")
+  end
+
+  # Returns the link-out URI for objects of "Nottingham Arabidopsis Stock Centre Seeds Database".
+  def self.NASC_code
+    RDF::URI.new("http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=")
+  end
+
+  # Returns the link-out URI for objects of "NCBI Gene".
+  def self.NCBI_Gene
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids=")
+  end
+
+  # Returns the link-out URI for objects of "NCBI databases".
+  def self.NCBI_gi
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
+  end
+
+  # Returns the link-out URI for objects of "NCBI GenPept".
+  def self.NCBI_GP
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=")
+  end
+
+  # Returns the link-out URI for objects of "Neuroscience Information Framework standard ontology, subcellular hierarchy".
+  def self.NIF_Subcellular
+    RDF::URI.new("http://www.neurolex.org/wiki/")
+  end
+
+  # Returns the link-out URI for objects of "National Microbial Pathogen Data Resource".
+  def self.NMPDR
+    RDF::URI.new("http://www.nmpdr.org/linkin.cgi?id=")
+  end
+
+  # Returns the link-out URI for objects of "Mendelian Inheritance in Man".
+  def self.OMIM
+    RDF::URI.new("http://omim.org/entry/")
+  end
+
+  # Returns the link-out URI for objects of "Genome Annotation Tool (Agrobacterium tumefaciens C58); PAMGO Interest Group".
+  def self.PAMGO_GAT
+    RDF::URI.new("http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=")
+  end
+
+  # Returns the link-out URI for objects of "Magnaporthe grisea database".
+  def self.PAMGO_MGG
+    RDF::URI.new("http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=")
+  end
+
+  # Returns the link-out URI for objects of "Virginia Bioinformatics Institute Microbial Database".
+  def self.PAMGO_VMD
+    RDF::URI.new("http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=")
+  end
+
+  # Returns the link-out URI for objects of "Protein ANalysis THrough Evolutionary Relationships".
+  def self.PANTHER
+    RDF::URI.new("http://pantree.org/node/annotationNode.jsp?id=")
+  end
+
+  # Returns the link-out URI for objects of "PathoSystems Resource Integration Center".
+  def self.PATRIC
+    RDF::URI.new("http://patric.vbi.vt.edu/gene/overview.php?fid=")
+  end
+
+  # Returns the link-out URI for objects of "Protein Data Bank".
+  def self.PDB
+    RDF::URI.new("http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=")
+  end
+
+  # Returns the link-out URI for objects of "Pfam database of protein families".
+  def self.Pfam
+    RDF::URI.new("http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?")
+  end
+
+  # Returns the link-out URI for objects of "Pharmacogenetics and Pharmacogenomics Knowledge Base".
+  def self.PharmGKB
+    RDF::URI.new("http://www.pharmgkb.org/do/serve?objId=")
+  end
+
+  # Returns the link-out URI for objects of "Protein Information Resource".
+  def self.PIR
+    RDF::URI.new("http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=")
+  end
+
+  # Returns the link-out URI for objects of "PIR Superfamily Classification System".
+  def self.PIRSF
+    RDF::URI.new("http://pir.georgetown.edu/cgi-bin/ipcSF?id=")
+  end
+
+  # Returns the link-out URI for objects of "Pubmed Central".
+  def self.PMCID
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=")
+  end
+
+  # Returns the link-out URI for objects of "PubMed".
+  def self.PMID
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/pubmed/")
+  end
+
+  # Returns the link-out URI for objects of "Plant Ontology Consortium Database".
+  def self.PO
+    RDF::URI.new("http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:")
+  end
+
+  # Returns the link-out URI for objects of "Plant Ontology custom references".
+  def self.PO_REF
+    RDF::URI.new("http://wiki.plantontology.org:8080/index.php/PO_REF:")
+  end
+
+  # Returns the link-out URI for objects of "PomBase".
+  def self.PomBase
+    RDF::URI.new("http://www.pombase.org/spombe/result/")
+  end
+
+  # Returns the link-out URI for objects of "Protein Ontology".
+  def self.PR
+    RDF::URI.new("http://www.proconsortium.org/cgi-bin/pro/entry_pro?id=PR:")
+  end
+
+  # Returns the link-out URI for objects of "PRINTS compendium of protein fingerprints".
+  def self.PRINTS
+    RDF::URI.new("http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=")
+  end
+
+  # Returns the link-out URI for objects of "ProDom protein domain families".
+  def self.ProDom
+    RDF::URI.new("http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=")
+  end
+
+  # Returns the link-out URI for objects of "Prosite database of protein families and domains".
+  def self.Prosite
+    RDF::URI.new("http://www.expasy.ch/cgi-bin/prosite-search-ac?")
+  end
+
+  # Returns the link-out URI for objects of "Pseudomonas Genome Project".
+  def self.PseudoCAP
+    RDF::URI.new("http://v2.pseudomonas.com/getAnnotation.do?locusID=")
+  end
+
+  # Returns the link-out URI for objects of "Proteomics Standards Initiative protein modification ontology".
+  def self.PSI_MOD
+    RDF::URI.new("http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:")
+  end
+
+  # Returns the link-out URI for objects of "NCBI PubChem database of bioassay records".
+  def self.PubChem_BioAssay
+    RDF::URI.new("http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=")
+  end
+
+  # Returns the link-out URI for objects of "NCBI PubChem database of chemical structures".
+  def self.PubChem_Compound
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=")
+  end
+
+  # Returns the link-out URI for objects of "NCBI PubChem database of chemical substances".
+  def self.PubChem_Substance
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=")
+  end
+
+  # Returns the link-out URI for objects of "Reactome - a curated knowledgebase of biological pathways".
+  def self.Reactome
+    RDF::URI.new("http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=")
+  end
+
+  # Returns the link-out URI for objects of "RefSeq".
+  def self.RefSeq
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
+  end
+
+  # Returns the link-out URI for objects of "RefSeq (Nucleic Acid)".
+  def self.RefSeq_NA
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
+  end
+
+  # Returns the link-out URI for objects of "RefSeq (Protein)".
+  def self.RefSeq_Prot
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=")
+  end
+
+  # Returns the link-out URI for objects of "Rfam database of RNA families".
+  def self.Rfam
+    RDF::URI.new("http://rfam.sanger.ac.uk/family/")
+  end
+
+  # Returns the link-out URI for objects of "Rat Genome Database".
+  def self.RGD
+    RDF::URI.new("http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=")
+  end
+
+  # Returns the link-out URI for objects of "Rhea, the Annotated Reactions Database".
+  def self.RHEA
+    RDF::URI.new("http://www.ebi.ac.uk/rhea/reaction.xhtml?id=")
+  end
+
+  # Returns the link-out URI for objects of "RNA Modification Database".
+  def self.RNAmods
+    RDF::URI.new("http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?")
+  end
+
+  # Returns the link-out URI for objects of "OBO Relation Ontology Ontology".
+  def self.RO
+    RDF::URI.new("http://purl.obolibrary.org/obo/RO_")
+  end
+
+  # Returns the link-out URI for objects of "SABIO Reaction Kinetics".
+  def self.SABIO_RK
+    RDF::URI.new("http://sabio.villa-bosch.de/reacdetails.jsp?reactid=")
+  end
+
+  # Returns the link-out URI for objects of "The SEED;".
+  def self.SEED
+    RDF::URI.new("http://www.theseed.org/linkin.cgi?id=")
+  end
+
+  # Returns the link-out URI for objects of "Saccharomyces Genome Database".
+  def self.SGD
+    RDF::URI.new("http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=")
+  end
+
+  # Returns the link-out URI for objects of "Saccharomyces Genome Database".
+  def self.SGD_LOCUS
+    RDF::URI.new("http://db.yeastgenome.org/cgi-bin/locus.pl?locus=")
+  end
+
+  # Returns the link-out URI for objects of "Saccharomyces Genome Database".
+  def self.SGD_REF
+    RDF::URI.new("http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=")
+  end
+
+  # Returns the link-out URI for objects of "Sol Genomics Network".
+  def self.SGN
+    RDF::URI.new("http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=")
+  end
+
+  # Returns the link-out URI for objects of "Sol Genomics Network".
+  def self.SGN_ref
+    RDF::URI.new("http://www.sgn.cornell.edu/chado/publication.pl?pub_id=")
+  end
+
+  # Returns the link-out URI for objects of "Simple Modular Architecture Research Tool".
+  def self.SMART
+    RDF::URI.new("http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=")
+  end
+
+  # Returns the link-out URI for objects of "Sequence Ontology".
+  def self.SO
+    RDF::URI.new("http://song.sourceforge.net/SOterm_tables.html#SO:")
+  end
+
+  # Returns the link-out URI for objects of "SUPERFAMILY protein annotation database".
+  def self.SUPERFAMILY
+    RDF::URI.new("http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/scop.cgi?ipid=SSF")
+  end
+
+  # Returns the link-out URI for objects of "UniProtKB/Swiss-Prot".
+  def self.Swiss_Prot
+    RDF::URI.new("http://www.uniprot.org/uniprot/")
+  end
+
+  # Returns the link-out URI for objects of "The Arabidopsis Information Resource".
+  def self.TAIR
+    RDF::URI.new("http://arabidopsis.org/servlets/TairObject?accession=")
+  end
+
+  # Returns the link-out URI for objects of "NCBI Taxonomy".
+  def self.taxon
+    RDF::URI.new("http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=")
+  end
+
+  # Returns the link-out URI for objects of "Transport Protein Database".
+  def self.TC
+    RDF::URI.new("http://www.tcdb.org/tcdb/index.php?tc=")
+  end
+
+  # Returns the link-out URI for objects of "Tetrahymena Genome Database".
+  def self.TGD_LOCUS
+    RDF::URI.new("http://db.ciliate.org/cgi-bin/locus.pl?locus=")
+  end
+
+  # Returns the link-out URI for objects of "Tetrahymena Genome Database".
+  def self.TGD_REF
+    RDF::URI.new("http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=")
+  end
+
+  # Returns the link-out URI for objects of "UniProtKB-TrEMBL protein sequence database".
+  def self.TrEMBL
+    RDF::URI.new("http://www.uniprot.org/uniprot/")
+  end
+
+  # Returns the link-out URI for objects of "Uber-anatomy ontology".
+  def self.UBERON
+    RDF::URI.new("http://purl.obolibrary.org/obo/UBERON_")
+  end
+
+  # Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database".
+  def self.UM_BBD_enzymeID
+    RDF::URI.new("http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=")
+  end
+
+  # Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database".
+  def self.UM_BBD_reactionID
+    RDF::URI.new("http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=")
+  end
+
+  # Returns the link-out URI for objects of "University of Minnesota Biocatalysis/Biodegradation Database".
+  def self.UM_BBD_ruleID
+    RDF::URI.new("http://umbbd.msi.umn.edu/servlets/rule.jsp?rule=")
+  end
+
+  # Returns the link-out URI for objects of "UniMod".
+  def self.UniMod
+    RDF::URI.new("http://www.unimod.org/modifications_view.php?editid1=")
+  end
+
+  # Returns the link-out URI for objects of "UniProt Archive".
+  def self.UniParc
+    RDF::URI.new("http://www.uniprot.org/uniparc/")
+  end
+
+  # Returns the link-out URI for objects of "UniPathway".
+  def self.UniPathway
+    RDF::URI.new("http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=")
+  end
+
+  # Returns the link-out URI for objects of "Universal Protein Knowledgebase".
+  def self.UniProtKB
+    RDF::URI.new("http://www.uniprot.org/uniprot/")
+  end
+
+  # Returns the link-out URI for objects of "UniProt Knowledgebase keywords".
+  def self.UniProtKB_KW
+    RDF::URI.new("http://www.uniprot.org/keywords/")
+  end
+
+  # Returns the link-out URI for objects of "UniProt Knowledgebase Subcellular Location vocabulary".
+  def self.UniProtKB_SubCell
+    RDF::URI.new("http://www.uniprot.org/locations/")
+  end
+
+  # Returns the link-out URI for objects of "Viral Bioinformatics Resource Center".
+  def self.VBRC
+    RDF::URI.new("http://vbrc.org/query.asp?web_id=VBRC:")
+  end
+
+  # Returns the link-out URI for objects of "Vertebrate Genome Annotation database".
+  def self.VEGA
+    RDF::URI.new("http://vega.sanger.ac.uk/perl/searchview?species=all&idx=All&q=")
+  end
+
+  # Returns the link-out URI for objects of "Virginia Bioinformatics Institute Microbial Database".
+  def self.VMD
+    RDF::URI.new("http://vmd.vbi.vt.edu/cgi-bin/browse/browserDetail_new.cgi?gene_id=")
+  end
+
+  # Returns the link-out URI for objects of "WormBase database of nematode biology".
+  def self.WB
+    RDF::URI.new("http://www.wormbase.org/db/gene/gene?name=")
+  end
+
+  # Returns the link-out URI for objects of "WormBase database of nematode biology".
+  def self.WB_REF
+    RDF::URI.new("http://www.wormbase.org/db/misc/paper?name=")
+  end
+
+  # Returns the link-out URI for objects of "Wikipedia".
+  def self.Wikipedia
+    RDF::URI.new("http://en.wikipedia.org/wiki/")
+  end
+
+  # Returns the link-out URI for objects of "Wormpep database of proteins of C. elegans".
+  def self.WP
+    RDF::URI.new("http://www.wormbase.org/db/get?class=Protein;name=WP:")
+  end
+
+  # Returns the link-out URI for objects of "Zebrafish Information Network".
+  def self.ZFIN
+    RDF::URI.new("http://zfin.org/cgi-bin/ZFIN_jump?record=")
+  end
+
+end
+
+end