biointerchange 0.2.0 → 0.2.1

data/README.md

@@ -163,7 +163,12 @@ To use the BioInterchange artifact, set-up add the following to your Maven POM f
       </dependency>
     </dependencies>
 
-Usage examples:
+Current vocabularies:
+
+*  Generic Feature Format Version 3 Ontology (GFF3O)
+*  Genome Variation Format Version 1 Ontology (GVF1O)
+
+Usage examples of accessing GFF3O's vocabulary:
 
     package org.biointerchange;
     
@@ -270,6 +275,9 @@ Building a new version of the Ruby vocabulary classes for GFF3, SIO, SOFA (requi
     echo -e "module BioInterchange\n" > lib/biointerchange/sio.rb
     ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sio> SIO >> lib/biointerchange/sio.rb
     echo -e "\nend" >> lib/biointerchange/sio.rb
+    echo -e "module BioInterchange\n" > lib/biointerchange/so.rb
+    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-so> SO >> lib/biointerchange/so.rb
+    echo -e "\nend" >> lib/biointerchange/so.rb
     echo -e "module BioInterchange\n" > lib/biointerchange/sofa.rb
     ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sofa> SOFA >> lib/biointerchange/sofa.rb
     echo -e "\nend" >> lib/biointerchange/sofa.rb
@@ -287,6 +295,7 @@ The source-code generation can be skipped, if none of the ontologies that are us
     ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gff3o> GFF3O | ruby generators/pythonify.rb > supplemental/python/biointerchange/gff3o.py
     ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gvf1o> GVF1O | ruby generators/pythonify.rb > supplemental/python/biointerchange/gvf1o.py
     ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sio> SIO | ruby generators/pythonify.rb > supplemental/python/biointerchange/sio.py
+    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-so> SO | ruby generators/pythonify.rb > supplemental/python/biointerchange/so.py
     ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sofa> SOFA | ruby generators/pythonify.rb > supplemental/python/biointerchange/sofa.py
     curl ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs | ruby generators/GOxrefify.rb | ruby generators/pythonify.rb > supplemental/python/biointerchange/goxref.py
 
@@ -308,6 +317,7 @@ The source-code generation can be skipped, if none of the ontologies that are us
     ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gff3o> GFF3O | ruby generators/javaify.rb > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GFF3O.java
     ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-gvf1o> GVF1O | ruby generators/javaify.rb > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GVF1O.java
     ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sio> SIO | ruby generators/javaify.rb > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SIO.java
+    ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-so> SO | ruby generators/javaify.rb "http://purl.obolibrary.org/obo/" > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SO.java
     ruby generators/rdfxml.rb <path-to-rdf/xml-version-of-sofa> SOFA | ruby generators/javaify.rb "http://purl.obolibrary.org/obo/" > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/SOFA.java
     curl ftp://ftp.geneontology.org/pub/go/doc/GO.xrf_abbs | ruby generators/GOxrefify.rb | ruby generators/javaify.rb > supplemental/java/biointerchange/src/main/java/org/biointerchange/vocabulary/GOXRef.java
 

data/VERSION

@@ -1 +1 @@
-0.2.0
+0.2.1

data/generators/javaify.rb

@@ -51,7 +51,7 @@ STDIN.each { |line|
     end
     transduction << "  public static #{line.sub('?', '').sub(/self\./, '').sub(/ *def\ /, '')}"
     method_name = transduction.sub(/^.*public static /m, '').sub(/(\(.*)?$/, '')
-    transduction.sub!("public static #{method_name}", "public static _#{method_name}_") if method_name.match(/^(true|false|class|public|private|static|return|if|while|do|clone|equals|toString|hashCode)$/)
+    transduction.sub!("public static #{method_name}", "public static _#{method_name}_") if method_name.match(/^(true|false|class|public|private|static|return|if|while|do|clone|equals|toString|hashCode|byte|char|short|int|long|float|double|boolean)$/)
     variables = transduction.scan(/^\s*public static \w+\((.+)\)$/)
     variables = variables[0][0].split(',').map { |variable| variable.strip } if variables.length > 0
     if method_name == 'is_object_property' then

data/generators/rdfxml.rb

@@ -80,8 +80,10 @@ model.keys.each { |key|
       comment = [ uri, "  # #{entry[OBO_DEF].to_s.sub(/^"(.*)" \[(.*)\]$/, '\1 (\2)').gsub(/\n|\r\n/, "\n  # ")}\n" ]
     elsif entry[RDF::RDFS.comment] then
       comment = [ uri, "  # #{entry[RDF::RDFS.comment].to_s.gsub(/\n|\r\n/, "\n  # ")}\n" ]
+    else
+      comment = [ uri, "  # -- No comment or description provided. --\n" ]
     end
-    comments[label_or_synonym] = set | [ comment ] if comment
+    comments[label_or_synonym] = set | [ comment ]
 
     set = combined_uris[label_or_synonym]
     set = [] unless set

data/lib/biointerchange/core.rb

@@ -24,6 +24,7 @@ module BioInterchange
   require 'biointerchange/goxref'
   require 'biointerchange/gvf1o'
   require 'biointerchange/sio'
+  require 'biointerchange/so'
   require 'biointerchange/sofa'
 
   # Reader/writer interfaces
@@ -89,21 +90,21 @@ module BioInterchange
     begin
       opt = Getopt::Long.getopts(
         ["--help", "-h", Getopt::BOOLEAN],
-        ["--debug", "-d", Getopt::BOOLEAN],  # set debug mode => print stack traces
+        ["--debug", "-d", Getopt::BOOLEAN],                     # set debug mode => print stack traces
         ["--no_rdf_graph_optimization", "-n", Getopt::BOOLEAN], # set self.skip_rdf_graph to false
-        ["--batchsize", "-b", Getopt::OPTIONAL], # batchsize for readers/writers that support +postpone?+
-        ["--input", "-i", Getopt::REQUIRED], # input file format
-        ["--rdf", "-r", Getopt::REQUIRED], # output file format
-        ["--annotate_name", Getopt::OPTIONAL], # name of resourcce/tool/person
-        ["--annotate_name_id", Getopt::OPTIONAL], # uri of resource/tool/person
-        ["--annotate_date", Getopt::OPTIONAL], # date of processing/annotation
-        ["--annotate_version", Getopt::OPTIONAL], # version number of resource
-        ["--file", "-f", Getopt::OPTIONAL], # file to read, will read from STDIN if not supplied
-        ["--out", "-o", Getopt::OPTIONAL], # output file, will out to STDOUT if not supplied
-        ["--version", "-v", Getopt::OPTIONAL] # output the version number of the gem and exit
+        ["--batchsize", "-b", Getopt::OPTIONAL],                # batchsize for readers/writers that support +postpone?+
+        ["--input", "-i", Getopt::REQUIRED],                    # input file format
+        ["--rdf", "-r", Getopt::REQUIRED],                      # output file format
+        ["--annotate_name", Getopt::OPTIONAL],                  # name of resourcce/tool/person
+        ["--annotate_name_id", Getopt::OPTIONAL],               # uri of resource/tool/person
+        ["--annotate_date", Getopt::OPTIONAL],                  # date of processing/annotation
+        ["--annotate_version", Getopt::OPTIONAL],               # version number of resource
+        ["--file", "-f", Getopt::OPTIONAL],                     # file to read, will read from STDIN if not supplied
+        ["--out", "-o", Getopt::OPTIONAL],                      # output file, will out to STDOUT if not supplied
+        ["--version", "-v", Getopt::BOOLEAN]                    # output the version number of the gem and exit
       )
       
-      if opt['help'] or not opt['input'] or not opt['rdf'] then
+      if opt['help'] or not (opt['input'] and opt['rdf'] or opt['version']) then
         puts "Usage: ruby #{$0} -i <format> -r <format> [options]"
         puts ''
         puts 'Supported input formats (--input <format>/-i <format>):'
@@ -154,7 +155,7 @@ module BioInterchange
       
       # Print version number and exit:
       if opt['version'] then
-        puts 'BioInterchange 0.1.4'
+        puts "BioInterchange #{Gem.loaded_specs["biointerchange"].version}"
         exit
       end
 

data/lib/biointerchange/genomics/gff3_rdf_ntriples.rb

@@ -145,6 +145,7 @@ protected
     return if @landmarks.has_key?(landmark.seqid)
     landmark_uri = RDF::URI.new("#{set_uri.to_s}/landmark/#{landmark.seqid}")
     @landmarks[landmark.seqid] = landmark_uri
+    graph.insert(RDF::Statement.new(landmark_uri, RDF.type, @base.Landmark))
     graph.insert(RDF::Statement.new(landmark_uri, @base.with_parent([ @base.id ].flatten, @base.landmark_properties)[0], RDF::Literal.new(landmark.seqid)))
     graph.insert(RDF::Statement.new(landmark_uri, @base.with_parent([ @base.start ].flatten, @base.landmark_properties)[0], RDF::Literal.new(landmark.start_coordinate))) if landmark.start_coordinate
     graph.insert(RDF::Statement.new(landmark_uri, @base.with_parent([ @base.end ].flatten, @base.landmark_properties)[0], RDF::Literal.new(landmark.end_coordinate))) if landmark.end_coordinate
@@ -164,16 +165,29 @@ protected
           graph.insert(RDF::Statement.new(feature_uri, @base.alias, RDF::Literal.new(value)))
         }
       elsif tag == 'Dbxref' then
-        feature_properties = @base.feature_properties.select { |uri| @base.is_object_property?(uri) }[0]
+        feature_properties = nil
+        if @base == BioInterchange::GFF3O then
+          feature_properties = @base.feature_properties.select { |uri| @base.is_datatype_property?(uri) }[0]
+        else
+          feature_properties = @base.feature_properties.select { |uri| @base.is_object_property?(uri) }[0]
+        end
         list.each { |value|
           begin
+            linkout = nil
+            # First: determine the Dbxref linkout URI as string
             if value.match(/^dbSNP(_\d+)?:rs\d+$/) then
-              graph.insert(RDF::Statement.new(feature_uri, @base.with_parent([ @base.dbxref ].flatten, feature_properties)[0], RDF::URI.new("http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=#{value.split(/:/)[1].sub(/^rs/, '')}")))
+              linkout = "http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=#{value.split(/:/)[1].sub(/^rs/, '')}"
             elsif value.match(/^COSMIC(_\d+)?:COSM\d+$/) then
-              graph.insert(RDF::Statement.new(feature_uri, @base.with_parent([ @base.dbxref ].flatten, feature_properties)[0], RDF::URI.new("http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=#{value.split(/:/)[1].sub(/^COSM/, '')}")))
+              linkout = "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=#{value.split(/:/)[1].sub(/^COSM/, '')}"
             else
               abbreviation, id = value.split(':', 2)
-              graph.insert(RDF::Statement.new(feature_uri, @base.with_parent([ @base.dbxref ].flatten, feature_properties)[0], RDF::URI.new(BioInterchange::GOXRef.send(BioInterchange.make_safe_label(abbreviation)).to_s + id)))
+              linkout = BioInterchange::GOXRef.send(BioInterchange.make_safe_label(abbreviation)).to_s + id
+            end
+            # Second, and finally: add a triple to the graph in the right representative format depending on the ontology used
+            if @base == BioInterchange::GFF3O then
+              graph.insert(RDF::Statement.new(feature_uri, @base.with_parent([ @base.dbxref ].flatten, feature_properties)[0], RDF::Literal.new(linkout, :datatype => RDF::XSD.anyURI )))
+            else
+              graph.insert(RDF::Statement.new(feature_uri, @base.with_parent([ @base.dbxref ].flatten, feature_properties)[0], RDF::URI.new(linkout))) if @base == BioInterchange::GVF1O
             end
           rescue NoMethodError
             raise BioInterchange::Exceptions::InputFormatError, 'Attribute Dbxref link-out is not resolvable, i.e. the name cannot be turned into an URL.'
@@ -198,12 +212,12 @@ protected
         list.each { |value|
           graph.insert(RDF::Statement.new(feature_uri, @base.note, RDF::Literal.new(value)))
         }
-      elsif tag == 'Ontology_term' and @base == BioInterchange::GFF3O then
+      elsif tag == 'Ontology_term' then
         list.each { |value|
           # TODO Sanitize values that are either not in GO xrf_abbs or need conversion to match
           #      match their associated Ruby method.
           namespace, accession = value.split(/:/, 2)
-          graph.insert(RDF::Statement.new(feature_uri, @base.ontology_term, RDF::URI.new("#{BioInterchange::GOXRef.send(namespace).to_s}#{accession}")))
+          graph.insert(RDF::Statement.new(feature_uri, @base.ontology_term, RDF::Literal.new("#{BioInterchange::GOXRef.send(namespace).to_s}#{accession}", :datatype => RDF::XSD.anyURI )))
         }
       elsif tag == 'Parent' then
         list.each { |parent_id|
@@ -225,6 +239,8 @@ protected
         graph.insert(RDF::Statement.new(target_uri, @base.with_parent([ @base.end ].flatten, target_object_properties)[0], @base.Positive)) if strand and strand == '+'
         graph.insert(RDF::Statement.new(target_uri, @base.with_parent([ @base.end ].flatten, target_object_properties)[0], @base.Negative)) if strand and strand == '-'
         graph.insert(RDF::Statement.new(feature_uri, @base.target, target_uri))
+      elsif tag == 'Variant_effect' and @base == BioInterchange::GVF1O then
+        serialize_variant_effects(graph, set_uri, feature_uri, list)
       elsif tag == 'Variant_seq' and @base == BioInterchange::GVF1O then
         serialize_variant_seqs(graph, set_uri, feature_uri, list)
       else
@@ -331,6 +347,28 @@ protected
     }
   end
 
+  # Serializes a list of variant effects.
+  #
+  # +graph+:: RDF graph to which the structured attribute is added
+  # +set_uri+:: the feature set URI to which the feature belongs to
+  # +feature_uri+:: the feature URI to the feature that is annotated with variant data
+  # +list+:: list of variant values
+  def serialize_variant_effects(graph, set_uri, feature_uri, list)
+    list.each_index { |index|
+      effect = list[index]
+      sequence_variant, variant_index, feature_type, feature_ids = effect.split(' ', 4)
+      feature_ids = feature_ids.split(' ')
+      effect_uri = RDF::URI.new("#{feature_uri.to_s}/variant/#{variant_index}/effect/#{index}")
+      serialize_variant_triple(graph, feature_uri, RDF::URI.new("#{feature_uri.to_s}/variant/#{variant_index}"), @base.effect, effect_uri)
+      graph.insert(RDF::Statement.new(effect_uri, RDF.type, @base.Effect))
+      graph.insert(RDF::Statement.new(effect_uri, @base.sequence_variant, BioInterchange::SO.send(BioInterchange.make_safe_label(sequence_variant))))
+      graph.insert(RDF::Statement.new(effect_uri, @base.feature_type, BioInterchange::SO.send(BioInterchange.make_safe_label(feature_type))))
+      feature_ids.each { |feature_id|
+        graph.insert(RDF::Statement.new(effect_uri, @base.feature, RDF::Literal.new(feature_id)))
+      }
+    }
+  end
+
   # Serializes a list of variant sequences.
   #
   # +graph+:: RDF graph to which the structured attribute is added
@@ -341,11 +379,25 @@ protected
     list.each_index { |index|
       value = list[index]
       variant_uri = RDF::URI.new("#{feature_uri.to_s}/variant/#{index}")
-      graph.insert(RDF::Statement.new(variant_uri, RDF.type, @base.Variant)) unless @variants.has_key?(variant_uri.to_s)
-      @variants[variant_uri.to_s] = true
-      graph.insert(RDF::Statement.new(variant_uri, @base.variant_seq, RDF::Literal.new(value)))
+      serialize_variant_triple(graph, feature_uri, variant_uri, @base.variant_seq, RDF::Literal.new(value))
     }
   end
+
+  # Adds a variant to the graph; tracks the variant's URI that RDF.type is only written out once.
+  #
+  # +graph+:: RDF graph to which the variant is added
+  # +feature_uri+:: the feature URI to the feature that is annotated with variant data
+  # +variant_uri+:: URI that identifies the feature in question ("subject", if you like)
+  # +predicate+:: predicate that describes the data being serialized
+  # +object+:: data to be serialized
+  def serialize_variant_triple(graph, feature_uri, variant_uri, predicate, object)
+    unless @variants.has_key?(variant_uri.to_s) then
+      graph.insert(RDF::Statement.new(feature_uri, @base.variant, variant_uri))
+      graph.insert(RDF::Statement.new(variant_uri, RDF.type, @base.Variant))
+    end
+    @variants[variant_uri.to_s] = true
+    graph.insert(RDF::Statement.new(variant_uri, predicate, object))
+  end
 end
 
 end

data/lib/biointerchange/genomics/gff3_reader.rb

@@ -97,7 +97,7 @@ protected
         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.'
+      raise BioInterchange::Exceptions::InputFormatError, "Type of feature is set to an unknown SOFA term: \"#{type}\""
     end
 
     # String to numeric value conversions:
@@ -166,6 +166,10 @@ protected
     end
   end
 
+  # Takes a GFF3/GVF attribute string (column 9) and decompose it into key/value pairs, where
+  # values are representing a list for the (possibly) comma separated GFF3/GVF attribute values.
+  #
+  # +attribute_string+:: key/value string (column 9) as seen in a GFF3/GVF file
   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 } }

data/lib/biointerchange/gff3o.rb

@@ -9,12 +9,6 @@ class GFF3O
     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)
@@ -79,18 +73,6 @@ class GFF3O
     return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') ]
   end
 
-  # A database cross-reference to associate a sequence alteration to its  representation in another database.
-  # (http://www.biointerchange.org/gff3o#GFF3_0034)
-  def self.dbxref
-    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0034')
-  end
-
-  # A cross-reference to an ontology term that is associated with a feature.
-  # (http://www.biointerchange.org/gff3o#GFF3_0035)
-  def self.ontology_term
-    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035')
-  end
-
   # Identifies the target that the features aligns to.
   # (http://www.biointerchange.org/gff3o#GFF3_0039)
   def self.target
@@ -125,6 +107,12 @@ class GFF3O
     return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0005')
   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:
   #   Start coordinate of the feature on the seqid landmark.
   #   (http://www.biointerchange.org/gff3o#GFF3_0007)
@@ -187,6 +175,18 @@ class GFF3O
     return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0029')
   end
 
+  # A database cross-reference to associate a sequence alteration to its representation in another database.
+  # (http://www.biointerchange.org/gff3o#GFF3_0034)
+  def self.dbxref
+    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0034')
+  end
+
+  # A cross-reference to an ontology term that is associated with a feature.
+  # (http://www.biointerchange.org/gff3o#GFF3_0035)
+  def self.ontology_term
+    return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035')
+  end
+
   # 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
@@ -235,6 +235,16 @@ class GFF3O
     return RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0053')
   end
 
+  # Either:
+  #   Sequence associated with this feature, if it has been specified using a FASTA string.
+  #   (http://www.biointerchange.org/gff3o#GFF3_0057)
+  # Or:
+  #   Sequence associated with this feature, if it has been specified using a FASTA string.
+  #   (http://www.biointerchange.org/gff3o#GFF3_0058)
+  def self.sequence
+    return [ RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0057'), RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0058') ]
+  end
+
   # Set of genomic sequence features, whose identifiers are unique within the set.
   # (http://www.biointerchange.org/gff3o#GFF3_0001)
   def self.Set
@@ -302,9 +312,6 @@ class GFF3O
     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
@@ -329,12 +336,6 @@ class GFF3O
     if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0026') then
       return true
     end
-    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0034') then
-      return true
-    end
-    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035') then
-      return true
-    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0039') then
       return true
     end
@@ -363,6 +364,9 @@ class GFF3O
     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
@@ -393,6 +397,12 @@ 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_0034') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035') then
+      return true
+    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0036') then
       return true
     end
@@ -432,6 +442,12 @@ class GFF3O
     if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0055') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0057') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0058') then
+      return true
+    end
     return false
   end
 
@@ -502,7 +518,7 @@ class GFF3O
   end
 
 private
-  @@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') }
+  @@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_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_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_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_0034') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0035') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , 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') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0057') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0028') , RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0058') => RDF::URI.new('http://www.biointerchange.org/gff3o#GFF3_0052') }
 
 end
 

data/lib/biointerchange/gvf1o.rb

@@ -12,12 +12,6 @@ class GVF1O
     return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0072') ]
   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/gvf1o#GVF1_0006)
-  def self.type
-    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006')
-  end
-
   # Either:
   #   Strand of the feature.
   #   (http://www.biointerchange.org/gvf1o#GVF1_0010)
@@ -108,12 +102,6 @@ class GVF1O
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0043')
   end
 
-  # Features that are affected by this sequence alteration effect.
-  # (http://www.biointerchange.org/gvf1o#GVF1_0044)
-  def self.feature
-    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044')
-  end
-
   # A coordinate range for ambiguous start coordinates.
   # (http://www.biointerchange.org/gvf1o#GVF1_0046)
   def self.start_range
@@ -178,10 +166,14 @@ class GVF1O
     return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0069'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0060') ]
   end
 
-  # Properties that are directly associated with Effect class instances.
-  # (http://www.biointerchange.org/gvf1o#GVF1_0070)
+  # Either:
+  #   Properties that are directly associated with Effect class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0070)
+  # Or:
+  #   Properties that are directly associated with Effect class instances.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0158)
   def self.effect_properties
-    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070')
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0070'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0158') ]
   end
 
   # Either:
@@ -220,12 +212,6 @@ class GVF1O
     return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0089'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0092') ]
   end
 
-  # A cross-reference to an ontology term that is associated with a feature.
-  # (http://www.biointerchange.org/gvf1o#GVF1_0096)
-  def self.ontology_term
-    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0096')
-  end
-
   # Either:
   #   Properties that are directly associated with TechnologyPlatform class instances.
   #   (http://www.biointerchange.org/gvf1o#GVF1_0102)
@@ -341,12 +327,24 @@ class GVF1O
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0150')
   end
 
+  # Identifies the target that the features aligns to.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0155)
+  def self.target
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0155')
+  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.
   # (http://www.biointerchange.org/gvf1o#GVF1_0005)
   def self.source
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005')
   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/gvf1o#GVF1_0006)
+  def self.type
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006')
+  end
+
   # Either:
   #   Start coordinate of the feature on the seqid landmark.
   #   (http://www.biointerchange.org/gvf1o#GVF1_0007)
@@ -459,6 +457,12 @@ class GVF1O
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039')
   end
 
+  # Features that are affected by this sequence alteration effect. This can be an external feature identifier, such as an Ensembl gene/transcript identifier.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0044)
+  def self.feature
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044')
+  end
+
   # Either:
   #   Unclear from GVF specification.
   #   (http://www.biointerchange.org/gvf1o#GVF1_0050)
@@ -523,6 +527,12 @@ class GVF1O
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0093')
   end
 
+  # A cross-reference to an ontology term that is associated with a feature.
+  # (http://www.biointerchange.org/gvf1o#GVF1_0096)
+  def self.ontology_term
+    return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0096')
+  end
+
   # An arbitrary comment. Free text.
   # (http://www.biointerchange.org/gvf1o#GVF1_0105)
   def self.comment
@@ -577,6 +587,16 @@ class GVF1O
     return RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0153')
   end
 
+  # Either:
+  #   Sequence associated with this feature, if it has been specified using a FASTA string.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0156)
+  # Or:
+  #   Sequence associated with this feature, if it has been specified using a FASTA string.
+  #   (http://www.biointerchange.org/gvf1o#GVF1_0157)
+  def self.sequence
+    return [ RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0156'), RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0157') ]
+  end
+
   # Set of genomic sequence features, whose identifiers are unique within the set.
   # (http://www.biointerchange.org/gvf1o#GVF1_0001)
   def self.Set
@@ -824,9 +844,6 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0004') then
       return true
     end
-    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006') then
-      return true
-    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0010') then
       return true
     end
@@ -863,9 +880,6 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0043') then
       return true
     end
-    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044') then
-      return true
-    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0046') then
       return true
     end
@@ -920,9 +934,6 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0091') then
       return true
     end
-    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0096') then
-      return true
-    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0102') then
       return true
     end
@@ -986,6 +997,9 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0152') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0155') then
+      return true
+    end
     return false
   end
 
@@ -996,6 +1010,9 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0005') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0006') then
+      return true
+    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0007') then
       return true
     end
@@ -1035,6 +1052,9 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0039') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0044') then
+      return true
+    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0048') then
       return true
     end
@@ -1107,6 +1127,9 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0095') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0096') then
+      return true
+    end
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0101') then
       return true
     end
@@ -1155,6 +1178,15 @@ class GVF1O
     if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0154') then
       return true
     end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0156') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0157') then
+      return true
+    end
+    if uri == RDF::URI.new('http://www.biointerchange.org/gvf1o#GVF1_0158') then
+      return true
+    end
     return false
   end
 
@@ -1315,7 +1347,7 @@ class GVF1O
   end
 
 private
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