Code for adding phenotypes and external ontology terms to mx.

phenotypes.rb

class AddPhenotypesAndOntologyRefs < ActiveRecord::Migration
  
  def self.up
    create_table :phenotypes do |table|
      table.string :type
      
      # common Phenotype attributes
      table.integer :entity_id # OntologyTerm or OntologyComposition
      table.string :entity_type # OntologyTerm or OntologyComposition
      
      # common CardinalPhenotype attributes (PresenceAbsence & Count)
      table.integer :within_entity_id # OntologyTerm or OntologyComposition
      table.string :within_entity_type # OntologyTerm or OntologyComposition
      
      # attributes for type=PresenceAbsencePhenotype
      table.boolean :is_present
      
      # attributes for type=CountPhenotype
      table.integer :minimum
      table.integer :maximum
      
      # attributes for type=QualitativePhenotype
      table.integer :quality_id # OntologyTerm or OntologyComposition
      table.string :quality_type # OntologyTerm or OntologyComposition
      table.integer :dependent_entity_id # OntologyTerm or OntologyComposition
      table.string :dependent_entity_type # OntologyTerm or OntologyComposition
    end
    
    create_table :ontology_terms do |table|
      table.string :uri
      table.string :label
      table.string :bioportal_ontology_id
      # more?
    end
    
    create_table :ontology_compositions do |table|
      table.integer :genus_id # OntologyTerm
    end
    
    create_table :differentiae do |table|
      table.integer :property_id # OntologyTerm
      table.integer :value_id # OntologyTerm or OntologyComposition
      table.string :value_type # OntologyTerm or OntologyComposition
      table.integer :ontology_composition_id # enclosing OntologyComposition
    end
    
  end

  def self.down
  end
  
end

class Phenotype < ActiveRecord::Base
  
  belongs_to :entity, :polymorphic => true
  
end

class CardinalPhenotype < Phenotype
  
  belongs_to :within_entity, :polymorphic => true
  
end

class PresenceAbsencePhenotype < CardinalPhenotype
  
end

class CountPhenotype < CardinalPhenotype
  
end

class QualitativePhenotype < Phenotype
  
  belongs_to :quality, :polymorphic => true
  belongs_to :dependent_entity, :polymorphic => true
  
end

class OntologyTerm < ActiveRecord::Base
  
end

class OntologyComposition < ActiveRecord::Base
  
  belongs_to :genus, :class_name => "OntologyTerm"
  has_many :differentiae
  
end

class OntologyTerm < ActiveRecord::Base
  
  belongs_to :property, :class_name => "OntologyTerm"
  belongs_to :value, :polymorphic => true
  belongs_to :ontology_composition
  
end