module EnsemblRest::Ontologies

Public Class Methods

ontology_ancestor(id, opts = {}) click to toggle source

Find all ancestors, all terms above, belonging to a given term

# File lib/bio-ensembl-rest/ontologies.rb, line 6
def self.ontology_ancestor(id, opts = {})
  return _ontology_id_generic id, 'ancestors_plain', opts
end
ontology_ancestor_chart(id, opts = {}) click to toggle source

Reconstruct the entire ancestory of a term from is_a and part_of relationships.

# File lib/bio-ensembl-rest/ontologies.rb, line 12
def self.ontology_ancestor_chart(id, opts = {})
  return _ontology_id_generic id, 'ancestors_chart', opts
end
ontology_descendents(id, opts = {}) click to toggle source

Find all descendents, all terms below, belonging to a given term.

# File lib/bio-ensembl-rest/ontologies.rb, line 18
def self.ontology_descendents(id, opts = {})
  return _ontology_id_generic id, 'descendents', opts
end
ontology_id(id, opts = {}) click to toggle source

Search for an ontological term by its namespaced identifier

# File lib/bio-ensembl-rest/ontologies.rb, line 24
def self.ontology_id(id, opts = {})
  return _ontology_id_generic id, 'plain', opts
end
ontology_name(name, opts = {}) click to toggle source

Search for a list of ontological terms by their name and an optional ontology

# File lib/bio-ensembl-rest/ontologies.rb, line 54
def self.ontology_name(name, opts = {})
  opts = EnsemblRest.parse_options opts
  path = EnsemblRest.build_path "/ontology/name/#{name}", opts
  
  if opts['content-type'] == 'ruby'
    plain_opts = opts.clone
    plain_opts['content-type'] = 'application/json'
    return JSON.parse ontology_name name, plain_opts
  end

  return EnsemblRest.fetch_data path, opts, 'ontologies'
end