biointerchange 0.1.2 → 0.1.3

data/lib/biointerchange/genomics/gvf_feature.rb

@@ -0,0 +1,24 @@
+module BioInterchange::Genomics
+
+# Represents a single genomic feature of a GVF file.
+class GVFFeature < GFF3Feature
+
+  # Creates a new feature representation. A feature is described on one line of the GVF file.
+  #
+  # +sequence_id+:: an identifier that determines the coordinate system for the feature
+  # +source+:: a text description of the origin of this feature description
+  # +type+:: either a SOFA accession, SOFA term, or textual description (the former are URIs, the latter is a string)
+  # +start_coordinate+:: an integer denoting the start coordinate of the feature
+  # +end_coordinate+:: an integer denoting the end coordinate of the feature, which is equal or larger than the start coordinate
+  # +score+:: a floating point score
+  # +strand+:: a constant determining whether the feature is NOT_STRANDED, the strand is UNKNOWN, or the feature is on the POSITIVE or NEGATIVE strand
+  # +attributes+:: a map of additional attributes associated with the feature
+  def initialize(sequence_id, source, type, start_coordinate, end_coordinate, score = nil, strand = NOT_STRANDED, attributes = {})
+    # Fill in phase, which is always omitted in GVF features (after 'strand', before 'attributes'):
+    super(sequence_id, source, type, start_coordinate, end_coordinate, score, strand, nil, attributes)
+  end
+
+end
+
+end
+

data/lib/biointerchange/genomics/gvf_feature_set.rb

@@ -0,0 +1,14 @@
+
+module BioInterchange::Genomics
+
+# A GVF feature set, which encapsules information of a single GVF file.
+class GVFFeatureSet < GFF3FeatureSet
+
+  def uri
+    super.sub(/^biointerchange:\/\/gff3\//, 'biointerchange://gvf/')
+  end
+
+end
+
+end
+

data/lib/biointerchange/genomics/gvf_pragmas.rb

@@ -0,0 +1,6 @@
+
+module BioInterchange::Genomics
+
+# TODO
+
+end

data/lib/biointerchange/genomics/gvf_reader.rb

@@ -0,0 +1,37 @@
+module BioInterchange::Genomics
+
+class GVFReader < GFF3Reader
+
+  # Creates a new instance of a Genome Variation Format (GVF) reader.
+  #
+  # +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)
+    # Remember: calling super without brackets passes all arguments of initialize!
+    super
+  end
+
+protected
+
+  def create_feature_set
+    BioInterchange::Genomics::GVFFeatureSet.new()
+  end
+
+  def add_pragma(feature_set, line)
+    line.chomp!
+    name, value = line[2..-1].split(/\s/, 2)
+    value.strip!
+
+    # Interpret pragmas, and if not known, delegate to GFF3Reader:
+    if name == 'gvf-version' then
+      feature_set.set_pragma(name, { name => value.to_f })
+    else
+      super(feature_set, line)
+    end
+  end
+
+end
+
+end
+

data/lib/biointerchange/gff3o.rb

@@ -488,7 +488,7 @@ 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_0025') , 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_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') }
 
 end
 

data/lib/biointerchange/gvf1o.rb

@@ -2,10 +2,17 @@ module BioInterchange
 
 class GVF1O
 
-  # Strand of the feature.
-  # (http://www.biointerchange.org/gvf1o#GVF1_0010)
+  # Either:
+  #   Strand of the feature.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0010)
+  # Or:
+  #   Strand of the breakpoint.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0083)
+  # Or:
+  #   Strand of a target -- if applicable.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0091)
   def self.strand
-    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010')
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0083'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0091') ]
   end
 
   # Tag name/value pair attributes of a feature.
@@ -32,8 +39,11 @@ class GVF1O
   # Or:
   #   FALDO "Region" instance replacement for a breakpoint's start, stop, strand properties.
   #   (http://www.biointerchange.org/gvf1o#GVF1_0079)
+  # Or:
+  #   FALDO "Region" instance replacement for a target's start, stop, strand  properties.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0090)
   def self.region
-    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0021'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079') ]
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0021'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0090') ]
   end
 
   # NCBI Taxonomy Ontology "NCBITaxon_1" (or sub-classes) instance that denotes the species for a feature set.
@@ -54,6 +64,12 @@ class GVF1O
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0036')
   end
 
+  # Zygosity of a variant.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0038)
+  def self.zygosity
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038')
+  end
+
   # An effect of a particular feature variant.
   # (http://www.biointerchange.org/gvf1o#GVF1_0041)
   def self.effect
@@ -164,6 +180,22 @@ class GVF1O
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0078')
   end
 
+  # Potential source or destination of zero-length sequence alterations.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0080)
+  def self.breakpoint
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0080')
+  end
+
+  # Either:
+  #   Properties that are directly associated with Target class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0089)
+  # Or:
+  #   Properties that are directly associated with Target class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0092)
+  def self.target_properties
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') ]
+  end
+
   # Either:
   #   ID of the landmark that establishes the coordinate system for a feature.
   #   (http://www.biointerchange.org/gvf1o#GVF1_0004)
@@ -195,8 +227,11 @@ class GVF1O
   # Or:
   #   Start coordinate of the feature on the seqid landmark.
   #   (http://www.biointerchange.org/gvf1o#GVF1_0073)
+  # Or:
+  #   Start coordinate of the target.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0094)
   def self.start
-    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0073') ]
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0073'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0094') ]
   end
 
   # Either:
@@ -208,8 +243,11 @@ class GVF1O
   # Or:
   #   End coordinate of the feature on the seqid landmark.
   #   (http://www.biointerchange.org/gvf1o#GVF1_0074)
+  # Or:
+  #   End coordinate of the target.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0095)
   def self.end
-    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0008'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0049'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0074') ]
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0008'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0049'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0074'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0095') ]
   end
 
   # Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features.
@@ -226,7 +264,7 @@ class GVF1O
 
   # Version of the GVF specification that defines the feature set contents.
   # (http://www.biointerchange.org/gvf1o#GVF1_0022)
-  def self.version
+  def self.gvf_version
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0022')
   end
 
@@ -284,12 +322,6 @@ class GVF1O
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0037')
   end
 
-  # Zygosity of a feature locus.
-  # (http://www.biointerchange.org/gvf1o#GVF1_0038)
-  def self.zygosity
-    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038')
-  end
-
   # Frequency of a variant in a population.
   # (http://www.biointerchange.org/gvf1o#GVF1_0039)
   def self.variant_freq
@@ -350,6 +382,24 @@ class GVF1O
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0076')
   end
 
+  # Version of the GFF specification that defines the feature set contents apart from GVF related definitions.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0081)
+  def self.gff_version
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0081')
+  end
+
+  # Creation date of the GVF file that this set stems from.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0082)
+  def self.file_date
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0082')
+  end
+
+  # ID or accession of the target alignment.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0093)
+  def self.target_id
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0093')
+  end
+
   # Set of genomic sequence features, whose identifiers are unique within the set.
   # (http://www.biointerchange.org/gvf1o#GVF1_0001)
   def self.Set
@@ -414,6 +464,18 @@ class GVF1O
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0058')
   end
 
+  # Denotes the zygosity of alleles.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0084)
+  def self.Zygosity
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0084')
+  end
+
+  # Indicates a feature's "target" of a nucleotide-to-nucleotide or protein-to-nucleotide alignment.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0088)
+  def self.Target
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0088')
+  end
+
   # Location on the positive (forward) strand.
   # (http://www.biointerchange.org/gvf1o#GVF1_0017)
   def self.Positive
@@ -438,6 +500,24 @@ class GVF1O
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0020')
   end
 
+  # Denotes heterozygous alleles.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0085)
+  def self.Heterozygous
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0085')
+  end
+
+  # Denotes homozygous alleles.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0086)
+  def self.Homozygous
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0086')
+  end
+
+  # Denotes hemizygous alleles.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0087)
+  def self.Hemizygous
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0087')
+  end
+
   # Determines whether the given URI is an object property.
   #
   # +uri+:: URI that is tested for being an object property
@@ -466,6 +546,9 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0036') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038') then
+      return true
+    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0041') then
       return true
     end
@@ -514,6 +597,21 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0080') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0083') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0090') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0091') then
+      return true
+    end
     return false
   end
 
@@ -572,9 +670,6 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0037') then
       return true
     end
-    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038') then
-      return true
-    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039') then
       return true
     end
@@ -638,6 +733,24 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0077') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0081') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0082') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0093') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0094') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0095') then
+      return true
+    end
     return false
   end
 
@@ -678,6 +791,12 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0058') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0084') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0088') then
+      return true
+    end
     return false
   end
 
@@ -697,6 +816,15 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0020') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0085') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0086') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0087') then
+      return true
+    end
     return false
   end
 
@@ -723,7 +851,7 @@ class GVF1O
   end
 
 private
-  @@parent_properties = { RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0012') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0014') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0015') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0021') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0023') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0034') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0036') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0041') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0042') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0043') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0046') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0047') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0051') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0067') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0053') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0078') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0008') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0009') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0013') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0064') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0022') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0024') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0025') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0026') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0027') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0029') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0030') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0031') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0032') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0037') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0065') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0061') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0049') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0061') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0050') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0054') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0055') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0056') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0057') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0073') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0074') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0076') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0077') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') }
+  @@parent_properties = { RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0012') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0014') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0015') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0021') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0023') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0068') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0034') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0036') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0038') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0041') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0042') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0043') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0046') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0047') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0051') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0067') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0053') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0078') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0079') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0080') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0066') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0083') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0075') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0090') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0091') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0008') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0009') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0013') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0064') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0022') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0024') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0025') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0026') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0027') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0029') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0030') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0062') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0031') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0032') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0037') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0065') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0061') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0049') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0061') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0050') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0054') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0055') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0056') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0057') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0073') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0074') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0071') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0076') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0077') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0059') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0081') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0082') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0063') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0093') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0094') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0095') => RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') , RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0088') => RDF::URI.new('http://www.w3.org/2002/07/owl#Thing') }
 
 end
 

data/lib/biointerchange/textmining/content.rb

@@ -63,6 +63,7 @@ class Content
     "biointerchange://textmining/content/#{@context.uri.sub(/^.*?:\/\//, '')}/#{@offset},#{@length},#{@type},#{process}"
   end
 
+
 end
 
 end

data/lib/biointerchange/textmining/content_connection.rb

@@ -0,0 +1,74 @@
+module BioInterchange::TextMining
+
+class ContentConnection
+
+  # Constants that describe content connection type.
+  UNSPECIFIED =  0
+  EQUIVALENCE =  1
+  SUBCLASS    =  2
+  THEME       =  3
+  SPECULATION =  4
+  NEGATION    =  5
+
+  # Creates a new document content connection representation between specific document content.
+  #
+  # +content1+:: document content 1
+  # +content2+:: document content 2
+  # +type+:: classifaction of the connection between the two document content objects
+  def initialize(content1, content2, type = UNSPECIFIED, process = nil)
+    if content1.nil? and content2.nil?
+      raise BioInterchange::Exceptions::ImplementationModelError, 'Content1 and Content2 can not both be nil'
+    elsif ( (! content1.kind_of?(BioInterchange::TextMining::Content)) && (! content1.kind_of?(BioInterchange::TextMining::ContentConnection)) && (! content1.nil?) )
+      raise BioInterchange::Exceptions::ImplementationModelError, 'Content1 has to be of kind BioInterchange::TextMining::Content or kind BioInterchange::TextMining::ContentConnection'  
+    elsif ( (! content2.kind_of?(BioInterchange::TextMining::Content)) && (! content2.kind_of?(BioInterchange::TextMining::ContentConnection)) && (! content2.nil?) )
+      raise BioInterchange::Exceptions::ImplementationModelError, 'Content2 has to be of kind BioInterchange::TextMining::Content or kind BioInterchange::TextMining::ContentConnection'  
+    end
+    @content1 = content1
+    @content2 = content2
+    @type = type
+    @process = process
+  end
+
+  # Sets the context of this content.
+  #
+  # +context+:: a +BioInterchange::TextMining::Document+ or +BioInterchange::TextMining::Content+ instance in which this content is enclosed in
+  def setContext(context)
+    @context = context
+  end
+
+  # Returns the offset of the content as absolute position within the document.
+  def content1
+    @content1
+  end
+
+  # Returns the length of the content, which is measured in characters.
+  def content2
+    @content2
+  end
+
+  # Returns the type of the content, if known, or +BioInterchange::TextMining::Content::UNSPECIFIED otherwise.
+  def type
+    @type
+  end
+
+  # Returns the process associated with this content, if previously provided, or nil otherwise.
+  def process
+    @process
+  end
+
+  # Returns a URI that identifies this content.
+  def uri
+    raise BioInterchange::Exceptions::ImplementationModelError, 'An URI can only be returned for content with a context (i.e., use setContext(context) first).' unless @context
+    process = '-'
+    c1 = '-'
+    c2 = '-'
+    process = "(#{@process.uri.sub(/^.*?:\/\//, '')})" if @process
+    c1 = "#{@content1.uri.sub(/^.*?:\/\//, '')}" if @content1
+    c2 = "#{@content2.uri.sub(/^.*?:\/\//, '')}" if @content2
+    "biointerchange://textmining/content_connection/#{@context.uri.sub(/^.*?:\/\//, '')}/#{c1},#{c2},#{@type},#{process}"
+  end
+
+end
+
+end
+