bio-ensembl 1.1.0

data/lib/bio-ensembl/db_connection.rb

@@ -0,0 +1,205 @@
+#
+# = ensembl/db_connection.rb - Connection classes for Ensembl databases
+#
+# Copyright::   Copyright (C) 2009 Jan Aerts <http://jandot.myopenid.com>
+#               Francesco Strozzi <francesco.strozzi@gmail.com>
+#                           
+# License::     The Ruby License
+#
+
+
+require 'rubygems'
+require 'active_record'
+
+
+class ActiveRecord::Base
+  def self.belongs_to_what
+    return self.reflect_on_all_associations(:belongs_to).collect{|a| a.name.to_s}
+  end
+  
+  def self.has_what
+    a = [self.reflect_on_all_associations(:has_one), self.reflect_on_all_associations(:has_many)]
+    return a.flatten.uniq.collect{|a| a.name.to_s}
+  end
+end
+
+
+module Ensembl
+  DB_ADAPTER = 'mysql'
+  DB_HOST = 'ensembldb.ensembl.org'
+  DB_USERNAME = 'anonymous'
+  DB_PASSWORD = ''
+  EG_HOST = 'mysql.ebi.ac.uk'
+  EG_PORT = 4157
+
+
+  # Generic class to perform dynamic connections to the Ensembl database and retrieve database names
+  class DummyDBConnection < ActiveRecord::Base
+    self.abstract_class = true
+    def self.connect(args)
+      self.establish_connection(
+                :adapter => args[:adapter] ||= Ensembl::DB_ADAPTER,
+                :host => args[:host] ||= Ensembl::DB_HOST,
+                :username => args[:username] ||= Ensembl::DB_USERNAME,
+                :password => args[:password] ||= Ensembl::DB_PASSWORD,
+                :port => args[:port],
+                :database => args[:database] ||= ''
+               )
+    end           
+  end
+
+  module DBRegistry 
+    # The Ensembl::Registry::Base is a super class providing general methods 
+    # to get database and connection info.
+    class Base < ActiveRecord::Base
+      self.abstract_class = true
+      self.pluralize_table_names = false
+            
+      def self.get_info
+        host,user,password,db_name,port = self.retrieve_connection.instance_values["connection_options"]
+        db_name =~/(\w+_\w+)_(core|variation|funcgen|compara)_(\d+)_\S+/
+        species,release = $1,$3 # just works for standard Ensembl database names
+        if species.nil? and release.nil? then
+          raise NameError, "Can't get database name from #{db_name}. Are you using non conventional names?"
+        else
+          return host,user,password,db_name,port,species,release.to_i
+        end
+      end
+      
+      # Method to retrieve the name of a database, using species, release and connection parameters
+      # passed by the user.    
+      def self.get_name_from_db(db_type,species,release,args)
+        species = species.underscore.tr(' ','_') # Always in lowercase. This keeps things simple when dealing with complex species names like in Ensembl Genomes database
+        dummy_db = DummyDBConnection.connect(args)
+        dummy_connection = dummy_db.connection
+        # check if a database exists with exactly the species name passed (regular way)
+        db_name = dummy_connection.select_values("SHOW DATABASES LIKE '%#{species}_#{db_type}_#{release.to_s}%'")[0]
+        # if a database is not found and we are working on Ensembl Genomes database...
+        if db_name.nil? and args[:ensembl_genomes] then
+          words = species.split(/_/)
+          first = words.shift
+          # ...try to find a collection database using the first name of the species passed (convention used for collection databases)
+          db_name = dummy_connection.select_values("SHOW DATABASES").select {|d| d=~/#{first}.*_collection_#{db_type}_#{release.to_s}/}[0]
+          # if a collection database match is found, then look inside to find the species
+          if db_name != nil then
+            dummy_db.disconnect! # close the generic connection with the host
+            args[:database] = db_name
+            dummy_db = DummyDBConnection.connect(args) # open a new connection directly with the collection database
+            species_name = species.gsub(first,first[0..0]) # transform the species name, so it can match the species names stored in the collection database
+            Ensembl::SESSION.collection_species = species_name # set the species used for this session, so it's easier to fetch slices from the genome of that species
+            
+            # check that the species passed is present in the collection database, otherwise returns a warning
+            exists = dummy_db.connection.select_values("SELECT species_id FROM meta WHERE LOWER(meta_value) = '#{species_name}' AND meta_key = 'species.db_name'")[0]
+            warn "WARNING: No species '#{species}' found in the database. Please check that the name is correct." if !exists
+          end
+        end
+        warn "WARNING: No connection to database established. Check that the species is in snake_case (was: #{species})." if db_name.nil?
+        return db_name
+      end
+      
+      def self.generic_connect(db_type, species, release, args = {})
+        
+        # check which release is used and load the correct VariationFeature version
+        require (release < 62) ? File.dirname(__FILE__) + '/variation/variation_feature.rb' : File.dirname(__FILE__) + '/variation/variation_feature62.rb'
+        Ensembl::SESSION.reset
+        Ensembl::SESSION.release = release
+        db_name = nil
+        # if the connection is established with Ensembl Genomes, set the default port and host
+        if args[:ensembl_genomes] then
+          args[:port] = EG_PORT
+          args[:host] = EG_HOST
+        end    
+        if args[:port].nil? then
+          args[:port] = ( release > 47 ) ? 5306 : 3306
+        end
+        if args[:database]
+          db_name = args[:database]
+        else 
+          db_name = self.get_name_from_db(db_type,species,release,args) # try to find the corresponding database 
+        end 
+        establish_connection(
+                            :adapter => args[:adapter] || Ensembl::DB_ADAPTER,
+                            :host => args[:host] || Ensembl::DB_HOST,
+                            :database => db_name,
+                            :username => args[:username] || Ensembl::DB_USERNAME,
+                            :password => args[:password] || Ensembl::DB_PASSWORD,
+                            :port => args[:port]
+                          )
+        
+        self.retrieve_connection # Check if the connection is working
+      
+      end      
+      
+    end
+    
+  end
+  
+  
+  module Core
+    # The Ensembl::Core::DBConnection is the actual connection established
+    # with the Ensembl server.
+    class DBConnection < Ensembl::DBRegistry::Base
+      self.abstract_class = true
+      self.pluralize_table_names = false
+      # The Ensembl::Core::DBConnection#connect method makes the connection
+      # to the Ensembl core database for a given species. By default, it connects
+      # to release 50 for that species. You _could_ use a lower number, but
+      # some parts of the API might not work, or worse: give the wrong results.
+      #
+      # @example
+      #  # Connect to release 50 of human
+      #  Ensembl::Core::DBConnection.connect('homo_sapiens')
+      #
+      #  # Connect to release 42 of chicken
+      #  Ensembl::Core::DBConnection.connect('gallus_gallus')
+      #
+      # @param [String] species Species to connect to. Must be in snake_case
+      # @param [Integer] ensembl_release. Release to connect to (default = 60)
+      def self.connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {})
+        self.generic_connect('core',species, release,args)
+      end
+      
+      def self.ensemblgenomes_connect(species, release = Ensembl::ENSEMBL_RELEASE, args={})
+        args[:ensembl_genomes] = true
+        self.generic_connect('core',species,release,args)
+      end
+
+      
+    end # Core::DBConnection
+
+  end # Core
+
+  module Variation
+    # The Ensembl::Variation::DBConnection is the actual connection established
+    # with the Ensembl server.
+    class DBConnection < Ensembl::DBRegistry::Base
+      self.abstract_class = true
+      self.pluralize_table_names = false
+      # The Ensembl::Variation::DBConnection#connect method makes the connection
+      # to the Ensembl variation database for a given species. By default, it connects
+      # to release 50 for that species. You _could_ use a lower number, but
+      # some parts of the API might not work, or worse: give the wrong results.
+      #
+      # @example
+      #  # Connect to release 50 of human
+      #  Ensembl::Variation::DBConnection.connect('homo_sapiens')
+      #
+      #  # Connect to release 42 of chicken
+      #  Ensembl::Variation::DBConnection.connect('gallus_gallus')
+      #
+      # @param [String] species Species to connect to. Must be in snake_case
+      # @param [Integer] ensembl_release. Release to connect to (default = 60)
+      def self.connect(species, release = Ensembl::ENSEMBL_RELEASE, args = {})
+        self.generic_connect('variation',species, release, args)
+      end
+      
+      def self.ensemblgenomes_connect(species, release = Ensembl::ENSEMBL_RELEASE, args={})
+        args[:ensembl_genomes] = true
+        self.generic_connect('variation',species,release,args)
+      end      
+
+    end # Variation::DBConnection
+    
+  end # Variation
+  
+end # Ensembl

data/lib/bio-ensembl/variation/activerecord.rb

@@ -0,0 +1,536 @@
+#
+# = ensembl/variation/activerecord.rb - ActiveRecord mappings to Ensembl Variation
+#
+# Copyright::   Copyright (C) 2008 Francesco Strozzi <francesco.strozzi@gmail.com>
+# License::     The Ruby License
+#
+# @author Francesco Strozzi
+
+nil
+module Ensembl
+  # The Ensembl::Variation module covers the variation databases from
+  # ensembldb.ensembl.org.
+  module Variation
+    # The Allele class describes a single allele of a variation. In addition to
+    # the nucleotide(s) (or absence of) that representing the allele frequency
+    # and population information may be present.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  allele = Allele.find(1)
+    #  puts allele.to_yaml
+    class Allele < DBConnection
+      set_primary_key 'allele_id'
+      belongs_to :sample
+      belongs_to :variation
+      belongs_to :population
+      belongs_to :subsnp_handle
+    end
+
+    # The AlleleGroup class represents a grouping of alleles that have tight 
+    # linkage and are usually present together. This is commonly known as a 
+    # Haplotype or Haplotype Block. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #  allele_group = AlleleGroup.find(1)
+    #  puts allele_group.to_yaml
+    class AlleleGroup < DBConnection
+      set_primary_key 'allele_group_id'
+      belongs_to :variation_group
+      belongs_to :source
+      belongs_to :sample
+      belongs_to :allele_group_allele
+    end
+    
+    # The AlleleGroupAllele class represents a connection class between Allele and AlleleGroup. 
+    # Should not be used directly.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class AlleleGroupAllele < DBConnection
+      belongs_to :variation
+      belongs_to :allele_group
+    end
+    
+    # Store information on attributes types
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class AttribType < DBConnection
+      set_primary_key "attrib_type_id"
+    end 
+    
+    # Store information on associated studies
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class AssociateStudy < DBConnection
+      set_primary_key "study1_id"
+      belongs_to :study
+    end
+    
+    
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class ConsequenceMapping < DBConnection
+      
+    end
+
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class FailedDescription < DBConnection
+      set_primary_key "failed_description_id"
+      has_many :failed_variations
+    end
+    
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class FailedVariation < DBConnection
+      set_primary_key "failed_variation_id"
+      belongs_to :failed_description
+      belongs_to :variation
+    end    
+    
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class FeatureType < DBConnection
+      set_primary_key "feature_type_id"
+    end
+        
+    class Meta < DBConnection
+      set_primary_key "meta_id"
+    end
+    
+    class MetaCoord < DBConnection
+     
+    end
+    
+    class Phenotype < DBConnection
+      set_primary_key "phenotype_id"
+      has_many :variation_annotations
+    end
+    
+    # The Sample class gives information about the biological samples stored in the database. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class Sample < DBConnection
+      set_primary_key "sample_id"
+      has_one :individual
+      has_one :sample_synonym
+      has_many :individual_genotype_multiple_bp
+      has_many :compressed_genotype_single_bp
+      has_many :read_coverage
+      has_one :population
+      has_many :tagged_variation_features
+    end
+
+    # The IndividualPopulation class is used to connect Individual and Population classes. 
+    # Should not be used directly.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class IndividualPopulation < DBConnection
+      belongs_to :individual, :foreign_key => "individual_sample_id"
+      belongs_to :population, :foreign_key => "population_sample_id"
+    end
+    
+    # The Individual class gives information on the single individuals used 
+    # to retrieve one or more biological samples.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class Individual < DBConnection
+      set_primary_key "sample_id"
+      belongs_to :sample
+      has_one :individual_type
+      has_many :individual_populations, :foreign_key => "individual_sample_id"
+      has_many :populations, :through => :individual_populations
+    end
+    
+    class IndividualGenotypeMultipleBp < DBConnection
+      belongs_to :sample
+      belongs_to :variation
+      belongs_to :subsnp_handle
+    end
+   
+    class IndividualType < DBConnection
+      set_primary_key "invidual_type_id"
+      belongs_to :individual
+    end    
+    
+    
+    class CompressedGenotypeSingleBp < DBConnection
+      belongs_to :population_genotype, :foreign_key => "sample_id"
+    end  
+    
+    class ReadCoverage < DBConnection
+      belongs_to :sample
+    end
+    
+    class Population < DBConnection
+      belongs_to :sample
+      set_primary_key "sample_id"
+      has_many :population_genotypes, :foreign_key => "sample_id"
+      has_many :individual_populations, :foreign_key => "population_sample_id"
+      has_many :individuals, :through => :individual_populations
+      has_many :sample_synonyms
+      has_one :population_structure
+      has_many :tagged_variation_features
+      has_many :alleles
+      has_many :allele_groups
+    end
+    
+    
+    # The PopulationStructure class gives information on super and sub populations
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class PopulationStructure < DBConnection
+      
+    end
+    
+    # The PopulationGenotype class gives information about alleles and allele 
+    # frequencies for a SNP observed within a population or a group of samples. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class PopulationGenotype < DBConnection
+      set_primary_key "population_genotype_id"
+      belongs_to :variation
+      belongs_to :population
+      belongs_to :subsnp_handle
+      has_many :compressed_genotype_single_bps, :foreign_key => "sample_id"
+    end
+    
+    # The ProteinInfo class gives information about protein translated from a given transcript. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class ProteinInfo < DBConnection
+      set_primary_key "protein_info_id"
+      belongs_to :transcript_variation
+      has_many :protein_positions
+    end
+    
+    # The PolyphenPrediction class gives information about variations effect predictions within an aminoacidic sequence 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class PolyphenPrediction < DBConnection
+      set_primary_key "polyphen_prediction_id"
+      belongs_to :protein_position
+    end  
+    
+    # The ProteinPosition class gives information about variations within an aminoacidic sequence. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class ProteinPosition < DBConnection
+      set_primary_key "protein_position_id"
+      belongs_to :protein_info
+      has_many :polyphen_predictions
+      has_many :sift_predictions
+    end
+    
+    
+    
+    # The SampleSynonym class represents information about alternative names 
+    # for sample entries. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class SampleSynonym < DBConnection
+      set_primary_key "sample_synonym_id"
+      belongs_to :source
+      belongs_to :sample
+      belongs_to :population
+    end
+    
+    # The Source class gives information on the different databases and SNP 
+    # panels used to retrieve the data
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class Source < DBConnection
+      set_primary_key "source_id"
+      has_many :sample_synonyms
+      has_many :allele_groups
+      has_many :variations
+      has_many :variation_groups
+      has_many :httags
+      has_many :variation_synonyms
+      has_many :variation_annotations
+      has_many :structural_variations
+      
+      def somatic_status # workaround as ActiveRecord do not parse SET field in MySQL
+        "#{attributes_before_type_cast['somatic_status']}" 
+      end
+      
+    end
+
+    # The StructuralVariation class gives information on structural variations mapped on the genome
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class StructuralVariation < DBConnection
+      set_primary_key "structural_variation_id"
+      belongs_to :source
+      belongs_to :seq_region
+      has_many :supporting_structural_variations
+      
+      class << self # Workaround for 'class' field, otherwise it creates a mess for AR
+        def instance_method_already_implemented?(method_name)
+          return true if method_name == 'class'
+          super
+        end
+      end
+      
+      def sv_class
+        self.attributes["class"]
+      end
+      
+    end
+    
+        
+    class SeqRegion < DBConnection
+      set_primary_key "seq_region_id"
+      has_many :variation_features
+      has_many :structural_variations
+    end
+    
+    # The SubsnpHandle class gives information on SNP Submitters
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class SupportingStructuralVariation < DBConnection
+      set_primary_key "supporting_structural_variation_id"
+      belongs_to :structural_variation
+    end
+    
+    # The SubsnpHandle class gives information on SNP Submitters
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class SubsnpHandle < DBConnection
+      set_primary_key "subsnp_id"
+      has_many :individual_genotype_multiple_bps, :foreign_key => "subsnp_id"
+      has_many :population_genotypes, :foreign_key => "subsnp_id"
+      has_many :alleles, :foreign_key => "subsnp_id"
+      has_many :variation_synonyms,:foreign_key => "subsnp_id"
+    end
+    
+    # The SiftPrediction class gives information about variations effect predictions within an aminoacidic sequence
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class SiftPrediction < DBConnection
+      set_primary_key "sift_prediction_id"
+      belongs_to :protein_position
+    end
+    
+    # The Study class gives information about studies producing variations information
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class Study < DBConnection
+      set_primary_key "study_id"
+      has_many :associate_studies, :foreign_key => "study1_id"
+      has_many :structural_variations
+      has_many :variation_annotations
+      
+      def study_type
+        "#{attributes_before_type_cast['study_type']}"
+      end
+      
+    end
+
+
+    # The Variation class represents single nucleotide polymorhisms (SNP) or variations 
+    # and provides information like the names (IDs), the validation status and 
+    # the allele information.
+    #
+    # *BUG*: fields like validation_status and consequence_type are created 
+    # using SET option directly in MySQL. These fields are bad interpreted by
+    # ActiveRecord, returning always 0.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    #
+    # @example
+    #   v = Variation.find_by_name('rs10111')
+    #   v.alleles.each do |a|
+    #     puts a.allele, a.frequency
+    #   end
+    #
+    #   variations = Variation.fetch_all_by_source('dbSNP') # many records
+    #   variations.each do |v|
+    #     puts v.name
+    #   end
+    # 
+    class Variation < DBConnection
+      set_primary_key "variation_id"
+      belongs_to :source
+      has_many :variation_synonyms
+      has_one :flanking_sequence
+      has_many :allele_group_alleles
+      has_many :allele_groups, :through => :allele_group_alleles
+      has_many :population_genotypes
+      has_many :alleles
+      has_many :variation_features
+      has_many :variation_group_variations
+      has_many :variation_groups, :through => :variation_group_variations
+      has_many :individual_genotype_multiple_bps
+      has_many :failed_variations
+      has_many :failed_descriptions, :through => :failed_variations
+      has_many :variation_set_variations
+      has_many :variation_sets, :through => :variation_set_variations
+
+      def self.fetch_all_by_source(source)
+        variations = Source.find_by_name(source).variations
+      end
+    end
+    
+    # The VariationSynonym class gives information on alterative names used 
+    # for Variation entries. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class VariationSynonym < DBConnection
+      set_primary_key "variation_synonym_id"
+      belongs_to :variation
+      belongs_to :source
+      belongs_to :subsnp_handle
+    end
+        
+    # The VariationGroup class represents a group of variations (SNPs) that are 
+    # linked and present toghether. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class VariationGroup < DBConnection
+      set_primary_key "variation_group_id"
+      belongs_to :source
+      has_one :variation_group_variation
+      has_one :httag
+      has_one :variation_group_feature
+      has_one :allele_group
+    end
+    
+    # The VariationGroupVariation class is a connection class. 
+    # Should not be used directly.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class VariationGroupVariation < DBConnection
+      belongs_to :variation
+      belongs_to :variation_group
+    end
+    
+    # The VariationGroupFeature class gives information on the genomic position 
+    # of each VariationGroup.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.    
+    class VariationGroupFeature < DBConnection
+      set_primary_key "variation_group_feature_id"
+      belongs_to :variation_group
+    end
+    
+    class VariationAnnotation < DBConnection
+      set_primary_key "variation_annotation_id"
+      belongs_to :variation
+      belongs_to :phenotype
+      belongs_to :source
+    end
+    
+    # The VariationSet class gives information on variations grouped by study, method, quality measure etc.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.   
+    class VariationSet < DBConnection
+      set_primary_key "variation_set_id"
+      has_many :variation_set_variations
+      has_many :variations, :through => :variation_set_variations
+    end
+    
+    class VariationSetVariation < DBConnection
+      belongs_to :variation
+      belongs_to :variation_set
+    end
+
+    # The VariationSet class gives information on super and sub VariationSets.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available. 
+    class VariationSetStructure < DBConnection
+      
+    end
+    
+    
+    
+    # The FlankingSequence class gives information about the genomic coordinates 
+    # of the flanking sequences, for a single VariationFeature. 
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class FlankingSequence < DBConnection
+      belongs_to :variation
+    end
+    
+    # The TaggedVariationFeature class is a connection class. 
+    # Should not be used directly.
+    #
+    # This class uses ActiveRecord to access data in the Ensembl database.
+    # See the general documentation of the Ensembl module for
+    # more information on what this means and what methods are available.
+    class TaggedVariationFeature < DBConnection
+      belongs_to :variation_feature
+      belongs_to :sample
+    end
+    
+    class Httag < DBConnection
+      set_primary_key "httag_id"
+      belongs_to :variation_group
+      belongs_to :source
+    end
+    
+  end
+end