Module: EnsemblREST::Ontology

Defined in:

lib/ensemblrest/ontoandtaxo.rb

Class Method Summary

• .ancestors(id, options = {}) ⇒ JSON

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

• .ancestors_chart(id, options = {}) ⇒ JSON

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

• .descendants(id, options = {}) ⇒ JSON

  Find all the terms descended from a given term.

• .id(name, options = {}) ⇒ JSON

  Search for an ontological term by its namespaced identifier.

• .name(name, options = {}) ⇒ JSON

  Search for a list of ontological terms by their name.

Class Method Details

.ancestors(id, options = {}) ⇒ JSON

Reconstruct the entire ancestry of a term from is_a and part_of relationships

Parameters:

• id (String) —

  An ontology term identifier

• options (Hash) (defaults to: {}) —

  Optional arguments for the service please goto rest.ensembl.org/documentation/info/ontology_ancestors

Returns:

• (JSON) —

  the entire ancestry of a term

# File 'lib/ensemblrest/ontoandtaxo.rb', line 23

def ancestors(id, options = {})
	return EnsemblREST.get("ontology/ancestors/#{id}", {format: 'json'}.merge(options))
end

.ancestors_chart(id, options = {}) ⇒ JSON

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

Parameters:

• id (String) —

  An ontology term identifier

• options (Hash) (defaults to: {}) —

  Optional arguments for the service please goto rest.ensembl.org/documentation/info/ontology_ancestors_chart

Returns:

• (JSON) —

  the entire ancestry of a term

# File 'lib/ensemblrest/ontoandtaxo.rb', line 32

def ancestors_chart(id, options = {})
	return EnsemblREST.get("ontology/ancestors/chart/#{id}", {format: 'json'}.merge(options))
end

.descendants(id, options = {}) ⇒ JSON

Find all the terms descended from a given term. By default searches are conducted within the namespace of the given identifier

Parameters:

• id (String) —

  An ontology term identifier

• options (Hash) (defaults to: {}) —

  Optional arguments for the service please goto rest.ensembl.org/documentation/info/ontology_descendants

Returns:

• (JSON) —

  the terms descended from a given term

# File 'lib/ensemblrest/ontoandtaxo.rb', line 41

def descendants(id, options = {})
	return EnsemblREST.get("ontology/descendants/#{id}", {format: 'json'}.merge(options))
end

.id(name, options = {}) ⇒ JSON

Search for an ontological term by its namespaced identifier

Parameters:

• name (String) —

  An ontology term identifier

• options (Hash) (defaults to: {}) —

  Optional arguments for the service please goto rest.ensembl.org/documentation/info/ontology_id

Returns:

• (JSON) —

  an ontological term

# File 'lib/ensemblrest/ontoandtaxo.rb', line 50

def id(name, options = {})
	return EnsemblREST.get("ontology/id/#{name}", {format: 'json'}.merge(options))
end

.name(name, options = {}) ⇒ JSON

Search for a list of ontological terms by their name

Parameters:

• name (String) —

  An ontology name. SQL wildcards are supported

• options (Hash) (defaults to: {}) —

  Optional arguments for the service please goto rest.ensembl.org/documentation/info/ontology_name

Returns:

• (JSON) —

  a list of ontological terms

# File 'lib/ensemblrest/ontoandtaxo.rb', line 59

def name(name, options = {})
	return EnsemblREST.get("ontology/name/#{URI.escape(name)}", {format: 'json'}.merge(options))
end