semtools 0.1.2 → 0.1.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 692ce02343cb00ac37bbc34476da08386bedf0eaca7946689eb62c9a1f06d555
+  metadata.gz: e68630d42a4faf01dc15fdfa9f1acd64425ef1396ed6f9ce0a8d76319922ba06
+  data.tar.gz: 952d908af5370031df0f19c98ab69fbb59b51825f050b69714f4494e15f77f77
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-  data.tar.gz: 46e5b49f611c021ee8576a522a0a6ef22a8b9ed349084dadb9e44fd76c712c05221e6314985f08bdba575ac2dd849f1f14d84d5ae686889f33fac993132a8372
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+  data.tar.gz: 2d0e0953f19d8c2cad2cc85a0c6d8c1cb9bf95f4dd1ee2d75aebcf15bdd3929d2938ede6544ed3f145ac5a8804b97af64f50a859ae7ecf8164f0ed4f07208fb2

data/bin/onto2json.rb

@@ -18,14 +18,20 @@ OptionParser.new do |opts|
   opts.banner = "Usage: #{__FILE__} [options]"
 
   options[:input_file] = nil
-  opts.on("-i", "--input_file PATH", "Input file with ontology in OBO format") do |data|
+  opts.on("-i", "--input_file FILE", "Input file with ontology in OBO format") do |data|
     options[:input_file] = data
   end
 
   options[:output_file] = nil
-  opts.on("-o", "--output_file PATH", "Output path") do |data|
+  opts.on("-o", "--output_file FILE", "Output path") do |data|
     options[:output_file] = data
   end
+
+  options[:build] = false
+  opts.on("-b", "--build", "Activate build mode (calculate dictionaries)") do
+    options[:build] = true
+  end
+
   
   opts.on_tail("-h", "--help", "Show this message") do
     puts opts
@@ -39,7 +45,7 @@ end.parse!
 # MAIN
 ##########################
 puts "Loading ontology ..."
-onto = Ontology.new(file: options[:input_file], load_file: true)
+onto = Ontology.new(file: options[:input_file], load_file: true, build: options[:build])
 puts "Exporting ontology to JSON ..."
 onto.write(options[:output_file])
 puts "Ontology exported"

data/lib/semtools/ontology.rb

@@ -2,2040 +2,2051 @@ require 'json'
 
 
 class Ontology
-	#########################################################
-	# AUTHOR NOTES
-	#########################################################
-
-	# 1 - Store @profiles as @stanzas[:instances]
-	# 2 - Items values (not keys) are imported as strings, not as symbols (maybe add a flag which indicates if values are, or not, symbols?) 
-
-
-	#############################################
-	# FIELDS
-	#############################################
-	# Handled class variables
-	# => @@basic_tags :: hash with main OBO structure tags
-	# => @@allowed_calcs :: hash with allowed ICs and similaritites calcs
-	# => @@symbolizable_ids :: tags which can be symbolized
-	# => @@tags_with_trailing_modifiers :: tags which can include extra info after specific text modifiers
-	#
-	# Handled object variables
-	# => @header :: file header (if is available)
-	# => @stanzas :: OBO stanzas {:terms,:typedefs,:instances}
-	# => @ancestors_index :: hash of ancestors per each term handled with any structure relationships
-	# => @descendants_index :: hash of descendants per each term handled with any structure relationships
-	# => @alternatives_index :: has of alternative IDs (include alt_id and obsoletes)
-	# => @obsoletes_index :: hash of obsoletes and it's new ids
-	# => @special_tags :: set of special tags to be expanded (:is_a, :obsolete, :alt_id)
-	# => @structureType :: type of ontology structure depending on ancestors relationship. Allowed: {atomic, sparse, circular, hierarchical}
-	# => @ics :: already calculated ICs for handled terms and IC types
-	# => @meta :: meta_information about handled terms like [ancestors, descendants, struct_freq, observed_freq]
-	# => @max_freqs :: maximum freqs found for structural and observed freqs
-	# => @dicts :: bidirectional dictionaries with three levels <key|value>: 1º) <tag|hash2>; 2º) <(:byTerm/:byValue)|hash3>; 3º) dictionary <k|v>
-	# => @profiles :: set of terms assigned to an ID
-	# => @profilesDict :: set of profile IDs assigned to a term
-	# => @items :: hash with items relations to terms
-	# => @removable_terms :: array of terms to not be considered
-	# => @term_paths :: metainfo about parental paths of each term
-
-	@@basic_tags = {ancestors: [:is_a], obsolete: :is_obsolete, alternative: [:alt_id,:replaced_by,:consider]}
-	@@allowed_calcs = {ics: [:resnik, :resnik_observed, :seco, :zhou, :sanchez], sims: [:resnik, :lin, :jiang_conrath]}
-	@@symbolizable_ids = [:id, :alt_id, :replaced_by, :consider]
-	@@tags_with_trailing_modifiers = [:is_a, :union_of, :disjoint_from, :relationship, :subsetdef, :synonymtypedef, :property_value]
-	@@multivalue_tags = [:alt_id, :is_a, :subset, :synonym, :xref, :intersection_of, :union_of, :disjoint_from, :relationship, :replaced_by, :consider, :subsetdef, :synonymtypedef, :property_value, :remark]
-	@@symbolizable_ids.concat(@@tags_with_trailing_modifiers)
-	
-	#############################################
-	# CONSTRUCTOR
-	#############################################
-	
-	# Instantiate a OBO_Handler object
-	# ===== Parameters
-	# +file+:: with info to be loaded (.obo ; .json)
-	# +load_file+:: activate load process automatically (only for .obo)
-	# +removable_terms+: term to be removed from calcs
-	def initialize(file: nil, load_file: false, removable_terms: [])
-		# Initialize object variables
-		@header = nil
-		@stanzas = {terms: {}, typedefs: {}, instances: {}}
-		@ancestors_index = {}
-		@descendants_index = {}
-		@alternatives_index = {}
-		@obsoletes_index = {}
-		@structureType = nil
-		@ics = Hash[@@allowed_calcs[:ics].map{|ictype| [ictype, {}]}]
-		@meta = {}
-		@special_tags = @@basic_tags.clone
-		@max_freqs = {:struct_freq => -1.0, :observed_freq => -1.0, :max_depth => -1.0}
-		@dicts = {}
-		@profiles = {}
-		@profilesDict = {}
-		@items = {}
-		@removable_terms = []
-		@term_paths = {}
-		# Load if proceeds
-		add_removable_terms(removable_terms) if !removable_terms.empty?
-		load(file) if load_file
-	end
-
-
-	#############################################
-	# CLASS METHODS
-	#############################################
-
-	# Expand a (starting) term using a specific tag and return all extended terms into an array and
-	# the relationship structuture observed (hierarchical or circular). If circular structure is
-	# foumd, extended array will be an unique vector without starting term (no loops).
-	# +Note+: we extremly recomend use get_related_ids_by_tag function instead of it (directly)
-	# ===== Parameters
-	# +start+:: term where start to expand
-	# +terms+:: set to be used to expand
-	# +target_tag+:: tag used to expand
-	# +eexpansion+:: already expanded info
-	# +split_info_char+:: special regex used to split info (if it is necessary)
-	# +split_info_indx+:: special index to take splitted info (if it is necessary)
-	# +alt_ids+:: set of alternative IDs
-	# ===== Returns 
-	# A vector with the observed structure (string) and the array with extended terms.
-	def self.get_related_ids(start_id, terms, target_tag, related_ids = {}, alt_ids = {})
-		# Take start_id term available info and already accumulated info
-		current_associations = related_ids[start_id]
-		current_associations = [] if current_associations.nil? 
-		return [:no_term,[]] if terms[start_id].nil?
-		id_relations = terms[start_id][target_tag]
-		return [:source,[]] if id_relations.nil?
-
-		# Prepare auxiliar variables
-		struct = :hierarchical
-
-		# Study direct extensions
-		id_relations = id_relations.clone
-		while id_relations.length > 0
-			id = id_relations.shift
-			id = alt_ids[id].first if alt_ids.include?(id) # NOTE: if you want to persist current ID instead source ID, re-implement this
-			
-			# Handle
-			if current_associations.include?(id) # Check if already have been included into this expansion
-				struct = :circular 
-			else
-				current_associations << id 
-				if related_ids.include?(id) # Check if current already has been expanded
-					current_associations = current_associations | related_ids[id]
-					if current_associations.include?(start_id) # Check circular case
-						struct = :circular
-						[id, start_id].each{|repeated| current_associations.delete(repeated)}
-					end	
-				else # Expand
-					related_ids[start_id] = current_associations
-					structExp, current_related_ids = self.get_related_ids(id, terms, target_tag, related_ids, alt_ids) # Expand current
-					current_associations = current_associations | current_related_ids
-					struct = :circular if structExp == :circular # Check struct				
-					if current_associations.include?(start_id) # Check circular case
-						struct = :circular
-						current_associations.delete(start_id)
-					end
-				end
-			end
-		end
-		related_ids[start_id] = current_associations
-
-		return struct, current_associations
-	end
-
-
-	# Expand terms using a specific tag and return all extended terms into an array and
-	# the relationship structuture observed (hierarchical or circular). If circular structure is
-	# foumd, extended array will be an unique vector without starting term (no loops) 
-	# ===== Parameters
-	# +terms+:: set to be used to expand
-	# +target_tag+:: tag used to expand
-	# +split_info_char+:: special regex used to split info (if it is necessary)
-	# +split_info_indx+:: special index to take splitted info (if it is necessary)
-	# +alt_ids+:: set of alternative IDs
-	# +obsoletes+:: integer with the number of obsolete IDs. used to calculate structure type.
-	# ===== Returns 
-	# A vector with the observed structure (string) and the hash with extended terms
-	def self.get_related_ids_by_tag(terms:,target_tag:, alt_ids: {}, obsoletes: 0)
-		# Define structure type
-		structType = :hierarchical
-		related_ids = {}
-		terms.each do |id, tags|
-			# Check if target tag is defined
-			if !tags[target_tag].nil?
-				# Obtain related terms
-				set_structure, _ = self.get_related_ids(id, terms, target_tag, related_ids, alt_ids)
-				# Check structure			
-				structType = :circular if set_structure == :circular
-			end
-		end
-
-		# Check special case
-		structType = :atomic if related_ids.length <= 0
-		structType = :sparse if related_ids.length > 0 && ((terms.length - related_ids.length - obsoletes) >= 2)
-		# Return type and hash with related_ids
-		return structType, related_ids
-	end
-
-
-	# Class method to transform string with <tag : info> into hash structure
-	# ===== Parameters
-	# +attributes+:: array tuples with info to be transformed into hash format
-	# ===== Returns 
-	# Attributes stored into hash structure
-	def self.info2hash(attributes, split_char = " ! ", selected_field = 0)
-		# Load info
-		info_hash = {}
-		# Only TERMS multivalue tags (future add Typedefs and Instance)
-		# multivalue_tags = [:alt_id, :is_a, :subset, :synonym, :xref, :intersection_of, :union_of, :disjoint_from, :relationship, :replaced_by, :consider]
-		attributes.each do |tag, value|
-			# Check
-			raise EncodingError, 'Info element incorrect format' if (tag.nil?) || (value.nil?)
-			# Prepare
-			tag = tag.lstrip.to_sym
-			value.lstrip!
-			value = value.split(split_char)[selected_field].to_sym if @@tags_with_trailing_modifiers.include?(tag)
-			
-			# Store
-			query = info_hash[tag]
-			if !query.nil? # Tag already exists
-				if !query.kind_of?(Array) # Check that tag is multivalue
-					raise('Attempt to concatenate plain text with another. The tag is not declared as multivalue. [' + tag.to_s + '](' + query + ')')
-				else
-					query << value	# Add new value to tag
-				end
-			else # New entry
-				if @@multivalue_tags.include?(tag)
-					info_hash[tag] = [value]
-				else
-					info_hash[tag] = value
-				end
-			end
-		end
-		self.symbolize_ids(info_hash)
-		return info_hash
-	end
-
-
-	# Class method to load an OBO format file (based on OBO 1.4 format). Specially focused on load
-	# the Header, the Terms, the Typedefs and the Instances.
-	# ===== Parameters
-	# +file+:: OBO file to be loaded
-	# ===== Returns 
-	# Hash with FILE, HEADER and STANZAS info
-	def self.load_obo(file) #TODO: Send to obo_parser class
-		raise("File is not defined") if file.nil?
-		# Data variables
-		header = ''
-		stanzas = {terms: {}, typedefs: {}, instances: {}}
-		# Auxiliar variables
-		infoType = 'Header'
-		currInfo = []
-		stanzas_flags = %w[[Term] [Typedef] [Instance]]
-		# Read file
-		File.open(file).each do |line|
-			line.chomp!
-			next if line.empty?
-			fields = line.split(':', 2)
-			# Check if new instance is found
-			if stanzas_flags.include?(line)
-				header = self.process_entity(header, infoType, stanzas, currInfo)
-				# Update info variables
-				currInfo = []
-				infoType = line.gsub!(/[\[\]]/, '')
-				next
-			end
-			# Concat info
-			currInfo << fields  
-		end
-		# Store last loaded info
-		header = self.process_entity(header, infoType, stanzas, currInfo) if !currInfo.empty?
-
-		# Prepare to return
-		finfo = {:file => file, :name => File.basename(file, File.extname(file))}
-		return finfo, header, stanzas
-	end
-
-
-	# Handle OBO loaded info and stores it into correct container and format
-	# ===== Parameters
-	# +header+:: container
-	# +infoType+:: current ontology item type detected
-	# +stanzas+:: container
-	# +currInfo+:: info to be stored
-	# ===== Returns 
-	# header newly/already stored
-	def self.process_entity(header, infoType, stanzas, currInfo)
-		info = self.info2hash(currInfo)
-		# Store current info
-		if infoType.eql?('Header')
-			header = info
-		else
-			id = info[:id]
-			case infoType
-				when 'Term'
-					stanzas[:terms][id] = info
-				when 'Typedef'
-					stanzas[:typedefs][id] = info
-				when 'Instance'
-					stanzas[:instances][id] = info
-			end
-		end
-		return header
-	end
-
-
-	# Symboliza all values into hashs using symbolizable tags as keys
-	# ===== Parameters
-	# +item_hash+:: hash to be checked
-	def self.symbolize_ids(item_hash)
-		@@symbolizable_ids.each do |tag|
-			query = item_hash[tag] 
-			if !query.nil?
-				if query.kind_of?(Array)
-					query.map!{|item| item.to_sym}
-				else
-					item_hash[tag] = query.to_sym if !query.nil?
-				end
-			end
-		end
-	end
-
-
-	#
-	# ===== Parameters
-	# +root+:: main term to expand
-	# +ontology+:: to be cutted
-	# +clone+:: if true, given ontology object will not be mutated
-	# +remove_up+:: if true, stores only the root term given an it descendants. If false, only root ancestors will be stored
-	# ===== Returns
-	# An Ontology object with terms after cut the ontology.
-	def self.mutate(root, ontology, clone: true, remove_up: true)
-		ontology = ontology.clone if clone
-		# Obtain affected IDs
-		descendants = ontology.descendants_index[root]
-		descendants << root # Store itself to do not remove it
-		# Remove unnecesary terms
-		ontology.stanzas[:terms] = ontology.stanzas[:terms].select{|id,v| remove_up ? descendants.include?(id) : !descendants.include?(id)}
-		ontology.ics = Hash[@@allowed_calcs[:ics].map{|ictype| [ictype, {}]}]
-		ontology.max_freqs = {:struct_freq => -1.0, :observed_freq => -1.0, :max_depth => -1.0}
-		ontology.dicts = {}
-		ontology.removable_terms = []
-		ontology.term_paths = {}
-		# Recalculate metadata
-		ontology.build_index
-		ontology.add_observed_terms_from_profiles
-		# Finish
-		return ontology
-	end
-
-
-
-	#############################################
-	# GENERAL METHODS
-	#############################################
-
-	# Include removable terms to current removable terms list
-	# ===== Parameters
-	# +terms+:: terms array to be concatenated
-	def add_removable_terms(terms)
-		terms = terms.map{|term| term.to_sym}
-		@removable_terms.concat(terms)
-	end
-
-
-	# Include removable terms to current removable terms list loading new
-	# terms from a one column plain text file
-	# ===== Parameters
-	# +file+:: to be loaded 
-	def add_removable_terms_from_file(file)
-		File.open(excluded_codes_file).each do |line|
-			line.chomp!
-			@removable_terms << line.to_sym
-		end
-	end
-
-	
-	# Increase observed frequency for a specific term
-	# ===== Parameters
-	# +term+:: term which frequency is going to be increased
-	# +increas+:: frequency rate to be increased. Default = 1
-	# ===== Return
-	# true if process ends without errors, false in other cases
-	def add_observed_term(term:,increase: 1.0)
-		# Check
-		raise ArgumentError, "Term given is NIL" if term.nil?
-		return false unless @stanzas[:terms].include?(term)
-		return false if @removable_terms.include?(term)
-		if @alternatives_index.include?(term)
-			alt_id = @alternatives_index[term]
-			@meta[alt_id] = {:ancestors => -1.0,:descendants => -1.0,:struct_freq => 0.0,:observed_freq => 0.0} if @meta[alt_id].nil?
-			@meta[term] = @meta[alt_id] 			
-		end
-		# Check if exists
-		@meta[term] = {:ancestors => -1.0,:descendants => -1.0,:struct_freq => 0.0,:observed_freq => 0.0} if @meta[term].nil?
-		# Add frequency
-		@meta[term][:observed_freq] = 0 if @meta[term][:observed_freq] == -1
-		@meta[term][:observed_freq] += increase
-		# Check maximum frequency
-		@max_freqs[:observed_freq] = @meta[term][:observed_freq] if @max_freqs[:observed_freq] < @meta[term][:observed_freq]  
-		return true
-	end
-
-
-	# Increase the arbitrary frequency of a given term set 
-	# ===== Parameters
-	# +terms+:: set of terms to be updated
-	# +increase+:: amount to be increased
-	# +transform_to_sym+:: if true, transform observed terms to symbols. Default: false
-	# ===== Return
-	# true if process ends without errors and false in other cases
-	def add_observed_terms(terms:, increase: 1.0, transform_to_sym: false)
-		# Check
-		raise ArgumentError, 'Terms array given is NIL' if terms.nil?
-		raise ArgumentError, 'Terms given is not an array' if !terms.is_a? Array
-		# Add observations
-		if transform_to_sym
-			checks = terms.map{|id| self.add_observed_term(term: id.to_sym,increase: increase)}
-		else
-			checks = terms.map{|id| self.add_observed_term(term: id,increase: increase)}
-		end
-		return checks
-	end
-
-
-	# Compare to terms sets 
-	# ===== Parameters
-	# +termsA+:: set to be compared
-	# +termsB+:: set to be compared
-	# +sim_type+:: similitude method to be used. Default: resnik
-	# +ic_type+:: ic type to be used. Default: resnik
-	# +bidirectional+:: calculate bidirectional similitude. Default: false
-	# ===== Return
-	# similitude calculated
-	def compare(termsA, termsB, sim_type: :resnik, ic_type: :resnik, bidirectional: true)
-		# Check
-		raise ArgumentError, "Terms sets given are NIL" if termsA.nil? | termsB.nil?
-		raise ArgumentError, "Set given is empty. Aborting similarity calc" if termsA.empty? | termsB.empty?
-		micasA = []
-		# Compare A -> B
-		termsA.each do |tA|
-			micas = termsB.map{|tB| self.get_similarity(tA, tB, type: sim_type, ic_type: ic_type)}
-			# Remove special cases
-			[false,nil].each do |err_value| micas.delete(err_value) end
-			# Obtain maximum value
-			micasA << micas.max if micas.length > 0
-			micasA << 0 if micas.length <= 0
-		end
-		means_sim = micasA.inject{ |sum, el| sum + el }.to_f / micasA.size
-		# Compare B -> A
-		if bidirectional
-			means_simA = means_sim * micasA.size
-			means_simB = self.compare(termsB, termsA, sim_type: sim_type, ic_type: ic_type, bidirectional: false) * termsB.size
-			means_sim = (means_simA + means_simB) / (termsA.size + termsB.size)
-		end
-		# Return
-		return means_sim
-	end
-
-
-	# Compare internal stored profiles against another set of profiles. If an external set is not provided, internal profiles will be compared with itself 
-	# ===== Parameters
-	# +external_profiles+:: set of external profiles. If nil, internal profiles will be compared with itself
-	# +sim_type+:: similitude method to be used. Default: resnik
-	# +ic_type+:: ic type to be used. Default: resnik
-	# +bidirectional+:: calculate bidirectional similitude. Default: false
-	# ===== Return
-	# Similitudes calculated
-	def compare_profiles(external_profiles: nil, sim_type: :resnik, ic_type: :resnik, bidirectional: true)
-		profiles_similarity = {} #calculate similarity between patients profile
-		profiles_ids = @profiles.keys
-		if external_profiles.nil?
-			comp_ids = profiles_ids
-			comp_profiles = @profiles
-			main_ids = comp_ids
-			main_profiles = comp_profiles
-		else
-			comp_ids = external_profiles.keys
-			comp_profiles = external_profiles
-			main_ids = profiles_ids
-			main_profiles = @profiles
-		end
-		# Compare
-		while !main_ids.empty?
-			curr_id = main_ids.shift
-			current_profile = main_profiles[curr_id]
-			comp_ids.each do |id|
-				profile = comp_profiles[id]
-				value = compare(current_profile, profile, sim_type: sim_type, ic_type: ic_type, bidirectional: bidirectional)
-				query = profiles_similarity[curr_id]
-				if query.nil?
-				  profiles_similarity[curr_id] = {id => value}
-				else
-				  query[id] = value
-				end
-			end    
-		end
-		return profiles_similarity
-	end
-
-
-	# Expand alternative IDs arround all already stored terms
-	# ===== Parameters
-	# +alt_tag+:: tag used to expand alternative IDs
-	# ===== Returns 
-	# true if process ends without errors and false in other cases
-	def get_index_alternatives(alt_tag: @@basic_tags[:alternative][0])
-		# Check input
-		raise('stanzas terms empty')  if @stanzas[:terms].empty?
-		# Take all alternative IDs
-		alt_ids2add = {}
-		@stanzas[:terms].each do |id, tags|
-			alt_ids = tags[alt_tag]
-			if !alt_ids.nil?
-				alt_ids = alt_ids - @removable_terms
-				# Update info
-				alt_ids.each do |alt_term|
-					@alternatives_index[alt_term] = id
-					alt_ids2add[alt_term] = @stanzas[:terms][id] if !@stanzas[:terms].include?(alt_term)
-					@ancestors_index[alt_term] = @ancestors_index[id] if !@ancestors_index[id].nil?
-				end
-			end
-		end
-		@stanzas[:terms].merge!(alt_ids2add)
-	end
-
-
-	# Executes basic expansions of tags (alternatives, obsoletes and parentals) with default values
-	# ===== Returns 
-	# true if eprocess ends without errors and false in other cases
-	def build_index()
-		self.get_index_alternatives
-		self.get_index_obsoletes
-		self.get_index_child_parent_relations
-			@alternatives_index.map{|k,v| @alternatives_index[k] = self.extract_id(v)}
-			@alternatives_index.compact!
-			@obsoletes_index.map{|k,v| @obsoletes_index[k] = self.extract_id(v)}
-			@obsoletes_index.compact!
-			@ancestors_index.map{|k,v| @ancestors_index[k] = v.map{|t| self.extract_id(t)}.compact}
-			@ancestors_index.compact!
-			@descendants_index.map{|k,v| @descendants_index[k] = v.map{|t| self.extract_id(t)}.compact}
-			@descendants_index.compact!
-		self.get_index_frequencies
-		self.calc_dictionary(:name)
-		self.calc_dictionary(:synonym, select_regex: /\"(.*)\"/)
-		self.calc_term_levels(calc_paths: true)
-	end
-
-
-	# Calculates regular frequencies based on ontology structure (using parentals)
-	# ===== Returns 
-	# true if everything end without errors and false in other cases
-	def get_index_frequencies()
-		# Check
-		if @ancestors_index.empty?
-			warn('ancestors_index object is empty') 
-		else
-			# Prepare useful variables
-			alternative_terms = @alternatives_index.keys
-			# Per each term, add frequencies
-			@stanzas[:terms].each do |id, tags|			
-				if @alternatives_index.include?(id)
-					alt_id = @alternatives_index[id]
-					query = @meta[alt_id] # Check if exist
-					if query.nil?
-						query = {ancestors: 0.0, descendants: 0.0, struct_freq: 0.0, observed_freq: 0.0}
-						@meta[alt_id] = query 
-					end 
-					@meta[id] = query
-					# Note: alternative terms do not increase structural frequencies
-				else # Official term
-					query = @meta[id] # Check if exist
-					if query.nil?
-						query = {ancestors: 0.0, descendants: 0.0, struct_freq: 0.0, observed_freq: 0.0}
-						@meta[id] = query 
-					end
-					# Store metadata
-					query[:ancestors] = @ancestors_index.include?(id) ? @ancestors_index[id].count{|anc| !alternative_terms.include?(anc)}.to_f : 0.0
-					query[:descendants] = @descendants_index.include?(id) ? @descendants_index[id].count{|desc| !alternative_terms.include?(desc)}.to_f : 0.0
-					query[:struct_freq] = query[:descendants] + 1.0
-					# Update maximums
-					@max_freqs[:struct_freq] = query[:struct_freq] if @max_freqs[:struct_freq] < query[:struct_freq]  
-					@max_freqs[:max_depth] = query[:descendants] if @max_freqs[:max_depth] < query[:descendants]  
-				end
-			end
-		end
-	end
-
-
-	# Expand obsoletes set and link info to their alternative IDs
-	# ===== Parameters
-	# +obs_tags+:: tags to be used to find obsoletes
-	# +alt_tags+:: tags to find alternative IDs (if are available)
-	# +reset_obsoletes+:: flag to indicate if obsoletes set must be reset. Default: true
-	# ===== Returns 
-	# true if process ends without errors and false in other cases
-	def get_index_obsoletes(obs_tag: @@basic_tags[:obsolete], alt_tags: @@basic_tags[:alternative])
-		if @stanzas[:terms].empty?
-			warn('stanzas terms empty')
-		else
-			# Check obsoletes
-			@stanzas[:terms].each do |id, term_tags|
-				next if term_tags.nil?
-				query = term_tags[obs_tag]
-				if !query.nil? && query == 'true' # Obsolete tag presence 
-					next if !@obsoletes_index[id].nil? # Already stored
-					# Check if alternative value is available
-					alt_ids = alt_tags.map{|alt| term_tags[alt]}.compact
-					if !alt_ids.empty?
-						alt_id = alt_ids.first.first #FIRST tag, FIRST id 
-						# Store
-						@alternatives_index[id] = alt_id
-						@obsoletes_index[id] = alt_id
-					end
-				end
-			end
-		end
-	end
-
-
-	# Expand parentals set and link all info to their alternative IDs. Also launch frequencies process
-	# ===== Parameters
-	# +tag+:: tag used to expand parentals
-	# +split_info_char+:: special regex used to split info (if it is necessary)
-	# +split_info_indx+:: special index to take splitted info (if it is necessary)
-	# ===== Returns 
-	# true if process ends without errors and false in other cases
-	def get_index_child_parent_relations(tag: @@basic_tags[:ancestors][0])
-		# Check
-		if @stanzas[:terms].nil?
-			warn('stanzas terms empty')
-		else
-			# Expand
-			structType, parentals = self.class.get_related_ids_by_tag(terms: @stanzas[:terms],
-															target_tag: tag,
-															alt_ids: @alternatives_index,
-															obsoletes: @obsoletes_index.length)
-			# Check
-			raise('Error expanding parentals')  if (structType.nil?) || parentals.nil?
-			# Prepare ancestors structure
-			anc = {}
-			des = {}
-			parentals.each do |id, parents|
-				parents = parents - @removable_terms
-				anc[id] = parents
-				parents.each do |anc_id| # Add descendants
-					if !des.include?(anc_id)
-						des[anc_id] = [id]
-					else 
-						des[anc_id] << id
-					end
-				end
-			end
-			# Store alternatives
-			@alternatives_index.each do |id,alt|
-				anc[id] = anc[alt] if anc.include?(alt)
-				des[id] = des[alt] if des.include?(alt)
-			end
-			# Check structure
-			if ![:atomic,:sparse].include? structType
-				structType = structType == :circular ? :circular : :hierarchical
-			end
-			# Store
-			@ancestors_index = anc
-			@descendants_index = des
-			@structureType = structType
-		end
-		# Finish		
-	end
-
-
-	# Find ancestors of a given term
-	# ===== Parameters
-	# +term+:: to be checked
-	# +filter_alternatives+:: if true, remove alternatives from final results
-	# ===== Returns 
-	# an array with all ancestors of given term or false if parents are not available yet
-	def get_ancestors(term, filter_alternatives = false)
-		return self.get_familiar(term, true, filter_alternatives)		
-	end
-
-
-	# Find descendants of a given term
-	# ===== Parameters
-	# +term+:: to be checked
-	# +filter_alternatives+:: if true, remove alternatives from final results
-	# ===== Returns 
-	# an array with all descendants of given term or false if parents are not available yet
-	def get_descendants(term, filter_alternatives = false)
-		return self.get_familiar(term, false, filter_alternatives)		
-	end
-
-
-	# Find ancestors/descendants of a given term
-	# ===== Parameters
-	# +term+:: to be checked
-	# +return_ancestors+:: return ancestors if true or descendants if false
-	# +filter_alternatives+:: if true, remove alternatives from final results
-	# ===== Returns 
-	# an array with all ancestors/descendants of given term or nil if parents are not available yet
-	def get_familiar(term, return_ancestors = true, filter_alternatives = false)
-		# Find into parentals
-		familiars = return_ancestors ? @ancestors_index[term] : @descendants_index[term]		
-		if !familiars.nil?
-			familiars = familiars.clone
-			if filter_alternatives
-				familiars.reject!{|fm| @alternatives_index.include?(fm)}
-			end
-		else
-			familiars = []
-		end
-		return familiars
-	end
-
-
-	# Obtain IC of an specific term
-	# ===== Parameters
-	# +term+:: which IC will be calculated
-	# +type+:: of IC to be calculated. Default: resnik
-	# +force+:: force re-calculate the IC. Do not check if it is already calculated
-	# +zhou_k+:: special coeficient for Zhou IC method
-	# ===== Returns 
-	# the IC calculated
-	def get_IC(termRaw, type: :resnik, force: false, zhou_k: 0.5)
-		term = termRaw.to_sym
-		# Check 
-		raise ArgumentError, "IC type specified (#{type}) is not allowed" if !@@allowed_calcs[:ics].include?(type)
-		# Check if it's already calculated
-		return @ics[type][term] if (@ics[type].include? term) && !force
-		# Calculate
-		ic = - 1
-		case type # https://arxiv.org/ftp/arxiv/papers/1310/1310.8059.pdf  |||  https://sci-hub.st/https://doi.org/10.1016/j.eswa.2012.01.082
-			###########################################
-			#### STRUCTURE BASED METRICS
-			###########################################
-			# Shortest path
-			# Weighted Link
-			# Hirst and St-Onge Measure
-			# Wu and Palmer
-			# Slimani
-			# Li
-			# Leacock and Chodorow
-			###########################################
-			#### INFORMATION CONTENT METRICS
-			###########################################
-			when :resnik # Resnik P: Using Information Content to Evaluate Semantic Similarity in a Taxonomy
-				# -log(Freq(x) / Max_Freq)
-				ic = -Math.log10(@meta[term][:struct_freq].fdiv(@max_freqs[:struct_freq]))
-			when :resnik_observed 
-				# -log(Freq(x) / Max_Freq)
-				ic = -Math.log10(@meta[term][:observed_freq].fdiv(@max_freqs[:observed_freq]))
-			# Lin
-			# Jiang & Conrath
-
-			###########################################
-			#### FEATURE-BASED METRICS
-			###########################################
-			# Tversky
-			# x-similarity
-			# Rodirguez
-
-			###########################################
-			#### HYBRID METRICS
-			###########################################
-			when :seco, :zhou # SECO:: An intrinsic information content metric for semantic similarity in WordNet
-				#  1 - ( log(hypo(x) + 1) / log(max_nodes) )
-				ic = 1 - Math.log10(@meta[term][:struct_freq]).fdiv(Math.log10(@stanzas[:terms].length - @alternatives_index.length))
-				if :zhou # New Model of Semantic Similarity Measuring in Wordnet				
-					# k*(IC_Seco(x)) + (1-k)*(log(depth(x))/log(max_depth))
-					@ics[:seco][term] = ic # Special store
-					ic = zhou_k * ic + (1.0 - zhou_k) * (Math.log10(@meta[term][:descendants]).fdiv(Math.log10(@max_freqs[:max_depth])))
-				end
-			when :sanchez # Semantic similarity estimation in the biomedical domain: An ontology-basedinformation-theoretic perspective
-				ic = -Math.log10((@meta[term][:descendants].fdiv(@meta[term][:ancestors]) + 1.0).fdiv(@max_freqs[:max_depth] + 1.0))
-			# Knappe
-		end			
-		@ics[type][term] = ic
-		return ic
-	end
-
-
-	# Calculates and return resnik ICs (by ontology and observed frequency) for observed terms
-	# ===== Returns 
-	# two hashes with resnik and resnik_observed ICs for observed terms
-	def get_observed_ics_by_onto_and_freq
-		# Chech there are observed terms
-		if @profiles.empty?
-			resnik = {}
-			resnik_observed = {}
-		else
-			# Calc ICs for all terms
-			observed_terms = @profiles.values.flatten.uniq
-			observed_terms.each{ |term| get_IC(term)}
-			observed_terms.each{ |term| get_IC(term, type: :resnik_observed)}
-			resnik = @ics[:resnik].select{|k,v| observed_terms.include?(k)}
-			resnik_observed = @ics[:resnik_observed].select{|k,v| observed_terms.include?(k)}
-		end
-		return resnik.clone, resnik_observed.clone
-	end
-
-
-	# Find the IC of the Most Index Content shared Ancestor (MICA) of two given terms
-	# ===== Parameters
-	# +termA+:: term to be cheked
-	# +termB+:: term to be checked
-	# +ic_type+:: IC formula to be used
-	# ===== Returns 
-	# the IC of the MICA(termA,termB)
-	def get_ICMICA(termA, termB, ic_type = :resnik)
-		mica = self.get_MICA(termA, termB, ic_type)
-		return mica.first.nil? ? nil : mica.last
-	end
-
-
-	# Find the Most Index Content shared Ancestor (MICA) of two given terms
-	# ===== Parameters
-	# +termA+:: term to be cheked
-	# +termB+:: term to be checked
-	# +ic_type+:: IC formula to be used
-	# ===== Returns 
-	# the MICA(termA,termB) and it's IC
-	def get_MICA(termA, termB, ic_type = :resnik)
-		termA = @alternatives_index[termA] if @alternatives_index.include?(termA)
-		termB = @alternatives_index[termB] if @alternatives_index.include?(termB)
-		mica = [nil,-1.0]
-		# Special case
-		if termA.eql?(termB)
-			ic = self.get_IC(termA, type: ic_type)
-			mica = [termA, ic]
-		else	
-			# Obtain ancestors (include itselfs too)
-			anc_A = self.get_ancestors(termA) 
-			anc_B = self.get_ancestors(termB)
-
-			if !(anc_A.empty? && anc_B.empty?)
-				anc_A << termA
-				anc_B << termB
-				# Find shared ancestors
-				shared_ancestors = anc_A & anc_B
-				# Find MICA
-				if shared_ancestors.length > 0
-					shared_ancestors.each do |anc|
-						ic = self.get_IC(anc, type: ic_type)
-						# Check
-						mica = [anc,ic] if ic > mica[1]
-					end
-				end
-			end
-		end
-		return mica
-	end
-
-
-	# Calculate similarity between two given terms
-	# ===== Parameters
-	# +termsA+:: to be compared
-	# +termsB+:: to be compared
-	# +type+:: similitude formula to be used
-	# +ic_type+:: IC formula to be used
-	# ===== Returns 
-	# the similarity between both sets or false if frequencies are not available yet
-	def get_similarity(termA, termB, type: :resnik, ic_type: :resnik)
-		# Check
-		raise ArgumentError, "SIM type specified (#{type}) is not allowed" if !@@allowed_calcs[:sims].include?(type)
-		sim = nil
-		# Launch comparissons
-		sim_res = get_ICMICA(termA, termB, ic_type)
-		if !sim_res.nil?
-			case type
-				when :resnik
-					sim = sim_res
-				when :lin
-					sim = (2.0 * sim_res).fdiv(self.get_IC(termA,type: ic_type) + self.get_IC(termB,type: ic_type))
-				when :jiang_conrath # This is not a similarity, this is a disimilarity (distance)
-					sim = (self.get_IC(termA, type: ic_type) + self.get_IC(termB, type: ic_type)) - (2.0 * sim_res)
-			end
-		end
-		return sim
-	end
-
-
-	# Method used to load information stored into an OBO file and store it into this object.
-	# If a file is specified by input parameter, current @file value is updated
-	# ===== Parameters
-	# +file+:: optional file to update object stored file
-	def load(file, build: true)
-		_, header, stanzas = self.class.load_obo(file)
-		@header = header
-		@stanzas = stanzas
-		self.remove_removable()
-		# @removable_terms.each{|removableID| @stanzas[:terms].delete(removableID)} if !@removable_terms.empty? # Remove if proceed
-		self.build_index() if build
-	end
-
-	# 
-	def remove_removable()
-		@removable_terms.each{|removableID| @stanzas[:terms].delete(removableID)} if !@removable_terms.empty? # Remove if proceed
-	end
-
-
-	# Exports an OBO_Handler object in json format
-	# ===== Parameters
-	# +file+:: where info will be stored
-	def write(file)
-		# Take object stored info
-		obj_info = {header: @header,
-					stanzas: @stanzas,
-					ancestors_index: @ancestors_index,
-					descendants_index: @descendants_index,
-					alternatives_index: @alternatives_index,
-					obsoletes_index: @obsoletes_index,
-					structureType: @structureType,
-					ics: @ics,
-					meta: @meta,
-					special_tags: @special_tags,
-					max_freqs: @max_freqs,
-					dicts: @dicts,
-					profiles: @profiles,
-					profilesDict: @profilesDict,
-					items: @items,
-					removable_terms: @removable_terms,
-					term_paths: @term_paths}
-		# Convert to JSON format & write
-		File.open(file, "w") { |f| f.write obj_info.to_json }
-	end
-
-
-	def is_number? string
-  		true if Float(string) rescue false
-	end
-
-
-	# Read a JSON file with an OBO_Handler object stored
-	# ===== Parameters
-	# +file+:: with object info
-	# ===== Return
-	# OBO_Handler internal fields 
-	def read(file)
-		# Read file
-		jsonFile = File.open(file)
-		jsonInfo = JSON.parse(jsonFile.read, :symbolize_names => true)
-		# Pre-process (Symbolize some hashs values)
-		jsonInfo[:stanzas][:terms].map{|id,info| self.class.symbolize_ids(info)} # STANZAS
-		jsonInfo[:stanzas][:typedefs].map{|id,info| self.class.symbolize_ids(info)}
-		jsonInfo[:stanzas][:instances].map{|id,info| self.class.symbolize_ids(info)}
-		jsonInfo[:alternatives_index] = jsonInfo[:alternatives_index].map{|id,value| [id, value.to_sym]}.to_h 
-		jsonInfo[:ancestors_index].map {|id,family_arr| family_arr.map!{|item| item.to_sym}}
-		jsonInfo[:descendants_index].map {|id,family_arr| family_arr.map!{|item| item.to_sym}}
-		jsonInfo[:obsoletes_index] = jsonInfo[:obsoletes_index].map{|id,value| [id, value.to_sym]}.to_h
-		jsonInfo[:dicts] = jsonInfo[:dicts].each do |flag, dictionaries|
-			# Special case: byTerm
-			dictionaries[:byTerm] = dictionaries[:byTerm].map do |term, value| 
-				if !term.to_s.scan(/\A[-+]?[0-9]*\.?[0-9]+\Z/).empty?  # Numeric dictionary
-					[term.to_s.to_i, value.map{|term| term.to_sym}]
-				elsif value.is_a? Numeric # Numeric dictionary
-					[term.to_sym, value]
-				elsif value.kind_of?(Array) && flag == :is_a
-					[term.to_sym, value.map{|v| v.to_sym}]
-				else
-					[term.to_sym, value]
-				end
-			end
-			dictionaries[:byTerm] = dictionaries[:byTerm].to_h
-			# By value
-			dictionaries[:byValue] = dictionaries[:byValue].map do |value, term| 
-				if value.is_a? Numeric # Numeric dictionary
-					[value, term.to_sym]
-				elsif term.is_a? Numeric # Numeric dictionary
-					[value.to_s.to_sym, term]
-				elsif flag == :is_a
-					[value.to_sym, term.map{|v| v.to_sym}]
-				elsif term.kind_of?(Array)
-					[value.to_sym, term.map{|t| t.to_sym}]
-				else
-					[value.to_s, term.to_sym]
-				end
-			end
-			dictionaries[:byValue] = dictionaries[:byValue].to_h
-		end 
-		jsonInfo[:profiles].map{|id,terms| terms.map!{|term| term.to_sym}}
-		jsonInfo[:profiles].keys.map{|id| jsonInfo[:profiles][id.to_s.to_i] = jsonInfo[:profiles].delete(id) if self.is_number?(id.to_s)}
-		jsonInfo[:profilesDict].map{|term,ids| ids.map!{|id| id.to_sym if !id.is_a?(Numeric)}}
-		jsonInfo[:removable_terms] = jsonInfo[:removable_terms].map{|term| term.to_sym}
-		jsonInfo[:special_tags] = jsonInfo[:special_tags].each do |k, v|
-			if v.kind_of?(Array)
-				jsonInfo[:special_tags][k] = v.map{|tag| tag.to_sym}
-			else
-				jsonInfo[:special_tags][k] = v.to_sym
-			end
-		end
-		jsonInfo[:items].each{|k,v| jsonInfo[:items][k] = v.map{|item| item.to_sym}}
-		jsonInfo[:term_paths].each{|term,info| jsonInfo[:term_paths][term][:paths] = info[:paths].map{|path| path.map{|t| t.to_sym}}}
-		# Store info
-		@header = jsonInfo[:header]
-		@stanzas = jsonInfo[:stanzas]
-		@ancestors_index = jsonInfo[:ancestors_index]
-		@descendants_index = jsonInfo[:descendants_index]
-		@alternatives_index = jsonInfo[:alternatives_index]
-		@obsoletes_index = jsonInfo[:obsoletes_index]
-		@structureType = jsonInfo[:structureType].to_sym
-		@ics = jsonInfo[:ics]
-		@meta = jsonInfo[:meta]
-		@special_tags = jsonInfo[:special_tags]
-		@max_freqs = jsonInfo[:max_freqs]
-		@dicts = jsonInfo[:dicts]
-		@profiles = jsonInfo[:profiles]
-		@profilesDict = jsonInfo[:profilesDict]
-		@items = jsonInfo[:items]
-		@removable_terms = jsonInfo[:removable_terms]
-		@term_paths = jsonInfo[:term_paths]
-	end
-
-
-	# Check if a given ID is stored as term into this object
-	# ===== Parameters
-	# +id+:: to be checked 
-	# ===== Return
-	# True if term is allowed or false in other cases
-	def exists? id
-		return stanzas[:terms].include?(id)
-	end
-
-
-	# This method assumes that a text given contains an allowed ID. And will try to obtain it splitting it
-	# ===== Parameters
-	# +text+:: to be checked 
-	# ===== Return
-	# The correct ID if it can be found or nil in other cases
-	def extract_id(text, splitBy: ' ')
-		if self.exists?(text)
-			return text
-		else
-			splittedText = text.to_s.split(splitBy).first.to_sym
-			return self.exists?(splittedText) ? splittedText : nil
-		end
-	end
-
-
-	# Generate a bidirectinal dictionary set using a specific tag and terms stanzas set
-	# This functions stores calculated dictionary into @dicts field.
-	# This functions stores first value for multivalue tags
-	# This function does not handle synonyms for byValue dictionaries
-	# ===== Parameters
-	# +tag+:: to be used to calculate dictionary
-	# +select_regex+:: gives a regfex that can be used to modify value to be stored
-	# +substitute_alternatives+:: flag used to indicate if alternatives must, or not, be replaced by it official ID
-	# +store_tag+:: flag used to store dictionary. If nil, mandatory tag given will be used
-	# +multiterm+:: if true, byValue will allows multi-term linkage (array)
-	# +self_type_references+:: if true, program assumes that refrences will be between Ontology terms, and it term IDs will be checked
-	# ===== Return
-	# void. And stores calcualted bidirectional dictonary into dictionaries main container
-	def calc_dictionary(tag, select_regex: nil, substitute_alternatives: true, store_tag: nil, multiterm: false, self_type_references: false)
-		tag = tag.to_sym
-		store_tag = tag if store_tag.nil?
-		if @stanzas[:terms].empty?
-			warn('Terms are not already loaded. Aborting dictionary calc') 
-		else
-			byTerm = {}
-			byValue = {}
-			# Calc per term
-			@stanzas[:terms].each do |term, tags|
-				referenceTerm = term
-				if @alternatives_index.include?(term) && substitute_alternatives # Special case
-					referenceTerm = @alternatives_index[term] if !@obsoletes_index.include?(@alternatives_index[term])
-				end
-				queryTag = tags[tag]
-				if !queryTag.nil?
-					# Pre-process
-					if !select_regex.nil?
-						if queryTag.kind_of?(Array)
-							queryTag = queryTag.map{|value| value.scan(select_regex).first}
-							queryTag.flatten!
-						else
-							queryTag = queryTag.scan(select_regex).first
-						end
-						queryTag.compact!
-					end
-					if queryTag.kind_of?(Array) # Store
-						if !queryTag.empty?
-							if byTerm.include?(referenceTerm)
-								byTerm[referenceTerm] = (byTerm[referenceTerm] + queryTag).uniq
-							else
-								byTerm[referenceTerm] = queryTag
-							end
-							if multiterm
-								queryTag.each do |value|
-									byValue[value] = [] if byValue[value].nil? 
-									byValue[value] << referenceTerm
-								end								
-							else
-								queryTag.each{|value| byValue[value] = referenceTerm}
-							end
-						end
-					else
-						if byTerm.include?(referenceTerm)
-							byTerm[referenceTerm] = (byTerm[referenceTerm] + [queryTag]).uniq
-						else
-							byTerm[referenceTerm] = [queryTag]
-						end
-						if multiterm
-							byValue[queryTag] = [] if byValue[queryTag].nil?
-							byValue[queryTag] << referenceTerm
-						else
-							byValue[queryTag] = referenceTerm
-						end
-					end
-				end
-			end
-			
-			# Check self-references
-			if self_type_references
-				byTerm.map do |term, references|
-					corrected_references = references.map do |t|
-						checked = self.extract_id(t)
-						if checked.nil?
-							t
-						else
-							byValue[checked] = byValue.delete(t) if checked != t && !byValue.keys.include?(checked) # Update in byValue
-							checked
-						end
-					end
-					byTerm[term] = corrected_references.uniq
-				end
-			end
-
-			# Check order
-			byTerm.map do |term,values|
-				if self.exists?(term)
-					referenceValue = @stanzas[:terms][term][tag]
-					if !referenceValue.nil?
-						if !select_regex.nil?
-							if referenceValue.kind_of?(Array)
-								referenceValue = referenceValue.map{|value| value.scan(select_regex).first}
-								referenceValue.flatten!
-							else
-								referenceValue = referenceValue.scan(select_regex).first
-							end
-							referenceValue.compact!
-						end
-						if self_type_references
-							if referenceValue.kind_of?(Array)
-								aux = referenceValue.map{|t| self.extract_id(t)}
-							else
-								aux = self.extract_id(referenceValue)
-							end
-							referenceValue = aux if !aux.nil?
-						end
-						referenceValue = [referenceValue] if !referenceValue.kind_of?(Array)
-						byTerm[term] = referenceValue + (values - referenceValue)
-					end
-				end
-			end
-
-			# Store
-			@dicts[store_tag] = {byTerm: byTerm, byValue: byValue}
-		end
-	end
-
-
-	# Calculates :is_a dictionary without alternatives substitution
-	def calc_ancestors_dictionary
-		self.calc_dictionary(:is_a, substitute_alternatives: false, self_type_references: true, multiterm: true)
-	end
-
-
-	# Translate a given value using an already calcualted dictionary
-	# ===== Parameters
-	# +toTranslate+:: value to be translated using dictiontionary
-	# +tag+:: used to generate the dictionary
-	# +byValue+:: boolean flag to indicate if dictionary must be used values as keys or terms as keys. Default: values as keys = true
-	# ===== Return
-	# translation
-	def translate(toTranslate, tag, byValue: true)
-		dict = byValue ? @dicts[tag][:byValue] : @dicts[tag][:byTerm]	
-		toTranslate =  get_main_id(toTranslate) if !byValue
-		return dict[toTranslate]
-	end
-
-
-	# Translate a name given
-	# ===== Parameters
-	# +name+:: to be translated
-	# ===== Return
-	# translated name or nil if it's not stored into this ontology
-	def translate_name(name)
-		term = self.translate(name, :name)
-		term = self.translate(name, :synonym) if term.nil?
-		return term			
-	end
-
-
-	# Translate several names and return translations and a list of names which couldn't be translated
-	# ===== Parameters
-	# +names+:: array to be translated
-	# ===== Return
-	# two arrays with translations and names which couldn't be translated respectively
-	def translate_names(names)
-		translated = []
-		rejected = []
-		names.each do |name|
-			tr = self.translate_name(name)
-			if tr.nil?
-				rejected << name
-			else
-				translated << tr
-			end
-		end
-		return translated, rejected
-	end
-
-
-	# Translates a given ID to it assigned name
-	# ===== Parameters
-	# +id+:: to be translated
-	# ===== Return
-	# main name or nil if it's not included into this ontology
-	def translate_id(id)
-		name = self.translate(id, :name, byValue: false)
-		return name.nil? ? nil : name.first
-	end
-
-
-	# Translates several IDs and returns translations and not allowed IDs list
-	# ===== Parameters
-	# +ids+:: to be translated
-	# ===== Return
-	# two arrays with translations and names which couldn't be translated respectively
-	def translate_ids(ids)
-		translated = []
-		rejected = []
-		ids.each do |term_id|
-			tr = self.translate_id(term_id.to_sym)
-			if !tr.nil?
-				translated << tr
-			else
-				rejected << tr
-			end
-		end
-		return translated, rejected
-	end
-
-
-	# ===== Returns 
-	# the main ID assigned to a given ID. If it's a non alternative/obsolete ID itself will be returned
-	# ===== Parameters
-	# +id+:: to be translated
-	# ===== Return
-	# main ID related to a given ID. Returns nil if given ID is not an allowed ID
-	def get_main_id(id)
-		return nil if !@stanzas[:terms].include? id
-		new_id = id
-		mainID = @alternatives_index[id]
-		new_id = mainID if !mainID.nil? & !@obsoletes_index.include?(mainID)
-		return new_id
-	end
-
-
-	# Check a pull of IDs and return allowed IDs removing which are not official terms on this ontology
-	# ===== Parameters
-	# +ids+:: to be checked
-	# ===== Return
-	# two arrays whit allowed and rejected IDs respectively
-	def check_ids(ids, substitute: true)
-		checked_codes = []
-		rejected_codes = []
-		ids.each do |id|
-			if @stanzas[:terms].include? id
-				if substitute
-					checked_codes << self.get_main_id(id)
-				else
-					checked_codes << id
-				end
-			else
-				rejected_codes << id
-			end
-		end
-		return checked_codes, rejected_codes
-	end
-
-
-	# Stores a given profile with an specific ID. If ID is already assigend to a profile, it will be replaced
-	# ===== Parameters
-	# +id+:: assigned to profile
-	# +terms+:: array of terms
-	# +substitute+:: subsstitute flag from check_ids
-	def add_profile(id, terms, substitute: true)
-		warn("Profile assigned to ID (#{id}) is going to be replaced") if @profiles.include? id
-		correct_terms, rejected_terms = self.check_ids(terms, substitute: substitute)
-		if !rejected_terms.empty?
-			warn('Given terms contains erroneus IDs. These IDs will be removed')
-		end
-		if id.is_a? Numeric
-			@profiles[id] = correct_terms  			
-		else
-			@profiles[id.to_sym] = correct_terms  
-		end
-	end	
-
-
-	# Method used to store a pull of profiles
-	# ===== Parameters
-	# +profiles+:: array/hash of profiles to be stored. If it's an array, numerical IDs will be assigned starting at 1 
-	# +calc_metadata+:: if true, launch calc_profiles_dictionary process
-	# +reset_stored+:: if true, remove already stored profiles
-	# +substitute+:: subsstitute flag from check_ids
-	def load_profiles(profiles, calc_metadata: true, reset_stored: false, substitute: false)
-		self.reset_profiles if reset_stored
-		# Check
-		if profiles.kind_of?(Array)
-			profiles.each_with_index do |items, i|
-				self.add_profile(i, items.map {|item| item.to_sym}, substitute: substitute)
-			end
-		else # Hash
-			if !profiles.keys.select{|id| @profiles.include?(id)}.empty?
-				warn('Some profiles given are already stored. Stored version will be replaced')
-			end
-			profiles.each{|id, prof| self.add_profile(id, prof, substitute: substitute)}
-		end
-
-		self.add_observed_terms_from_profiles(reset: true)
-
-		if calc_metadata
-			self.calc_profiles_dictionary
-		end
-	end
-
-
-	# Internal method used to remove already stored profiles and restore observed frequencies
-	def reset_profiles
-		# Clean profiles storage
-		@profiles = {}
-		# Reset frequency observed
-		@meta.each{|term,info| info[:observed_freq] = 0}
-		@max_freqs[:observed_freq] = 0
-	end
-
-
-	# ===== Returns 
-	# profiles assigned to a given ID
-	# ===== Parameters
-	# +id+:: profile ID
-	# ===== Return
-	# specific profile or nil if it's not stored
-	def get_profile(id)
-		return @profiles[id]
-	end	
-
-
-	# ===== Returns 
-	# an array of sizes for all stored profiles
-	# ===== Return
-	# array of profile sizes
-	def get_profiles_sizes()
-		return @profiles.map{|id,terms| terms.length}
-	end
-
-
-	# ===== Returns 
-	# mean size of stored profiles
-	# ===== Parameters
-	# +round_digits+:: number of digits to round result. Default: 4
-	# ===== Returns 
-	# mean size of stored profiles
-	def get_profiles_mean_size(round_digits: 4)
-		sizes = self.get_profiles_sizes
-		return sizes.inject(0){|sum, n| sum + n}.fdiv(@profiles.length).round(round_digits)
-	end
-
-
-	# Calculates profiles sizes and returns size assigned to percentile given
-	# ===== Parameters
-	# +perc+:: percentile to be returned
-	# +increasing_sort+:: flag to indicate if sizes order must be increasing. Default: false
-	# ===== Returns 
-	# values assigned to percentile asked
-	def get_profile_length_at_percentile(perc=50, increasing_sort: false)
-		prof_lengths = self.get_profiles_sizes.sort
-		prof_lengths.reverse! if !increasing_sort
-		n_profiles = prof_lengths.length 
-		percentile_index = ((perc * (n_profiles - 1)).fdiv(100) - 0.5).round # Take length which not overpass percentile selected
-		percentile_index = 0 if percentile_index < 0 # Special case (caused by literal calc)
-		return prof_lengths[percentile_index]
-	end
-
-
-	# Translate a given profile to terms names
-	# ===== Parameters
-	# +prof+:: array of terms to be translated
-	# ===== Returns 
-	# array of translated terms. Can include nils if some IDs are not allowed
-	def profile_names(prof)
-		return prof.map{|term| self.translate_id(term)}
-	end
-
-
-	# Trnaslates a bunch of profiles to it sets of term names
-	# ===== Parameters
-	# +profs+:: array of profiles
-	# +asArray+:: flag to indicate if results must be returned as: true => an array of tuples [ProfID, ArrayOdNames] or ; false => hashs of translations
-	# ===== Returns 
-	# translated profiles
-	def translate_profiles_ids(profs = [], asArray: true)
-		profs = @profiles if profs.empty?
-		profs = profs.each_with_index.map{|terms, index| [index, terms]}.to_h if profs.kind_of?(Array)
-		profs_names = profs.map{|id, terms| [id, self.profile_names(terms)]}.to_h
-		return asArray ? profs_names.values : profs_names
-	end
-
-
-	# Includes as "observed_terms" all terms included into stored profiles
-	# ===== Parameters
-	# +reset+:: if true, reset observed freqs alreeady stored befor re-calculate
-	def add_observed_terms_from_profiles(reset: false)
-		@meta.each{|term, freqs| freqs[:observed_freq] = -1} if reset
-		@profiles.each{|id, terms| self.add_observed_terms(terms: terms)}
-	end
-
-
-	# Get a term frequency
-	# ===== Parameters
-	# +term+:: term to be checked
-	# +type+:: type of frequency to be returned. Allowed: [:struct_freq, :observed_freq]
-	# ===== Returns 
-	# frequency of term given or nil if term is not allowed
-	def get_frequency(term, type: :struct_freq)
-		queryFreq = @meta[term]
-		return queryFreq.nil? ? nil : queryFreq[type]		
-	end
-
-
-	# Geys structural frequency of a term given
-	# ===== Parameters
-	# +term+:: to be checked
-	# ===== Returns 
-	# structural frequency of given term or nil if term is not allowed
-	def get_structural_frequency(term)
-		return self.get_frequency(term, type: :struct_freq)
-	end
-
-
-	# Gets observed frequency of a term given
-	# ===== Parameters
-	# +term+:: to be checked
-	# ===== Returns 
-	# observed frequency of given term or nil if term is not allowed
-	def get_observed_frequency(term)
-		return self.get_frequency(term, type: :observed_freq)
-	end
-
-
-	# Calculates frequencies of stored profiles terms
-	# ===== Parameters
-	# +ratio+:: if true, frequencies will be returned as ratios between 0 and 1.
-	# +literal+:: if true, literal terms will be used to calculate frequencies instead translate alternative terms
-	# +asArray+:: used to transform returned structure format from hash of Term-Frequency to an array of tuples [Term, Frequency]
-	# +translate+:: if true, term IDs will be translated to 
-	# ===== Returns 
-	# stored profiles terms frequencies
-	def get_profiles_terms_frequency(ratio: true, literal: true, asArray: true, translate: true)
-		n_profiles = @profiles.length
-		if literal
-			freqs = {}
-			@profiles.each do |id, terms|
-				terms.each do |literalTerm|
-					if freqs.include?(literalTerm)
-						freqs[literalTerm] += 1
-					else
-						freqs[literalTerm] = 1
-					end
-				end
-			end
-			if (ratio || translate)
-				aux_keys = freqs.keys
-				aux_keys.each do |term| 
-					freqs[term] = freqs[term].fdiv(n_profiles) if ratio
-					if translate
-						tr = self.translate_id(term)
-						freqs[tr] = freqs.delete(term) if !tr.nil?
-					end
-				end
-			end
-			if asArray
-				freqs = freqs.map{|term, freq| [term, freq]}
-				freqs.sort!{|h1, h2| h2[1] <=> h1[1]}
-			end
-		else # Freqs translating alternatives
-			freqs = @meta.select{|id, freqs| freqs[:observed_freq] > 0}.map{|id, freqs| [id, ratio ? freqs[:observed_freq].fdiv(n_profiles) : freqs[:observed_freq]]}
-			freqs = freqs.to_h if !asArray
-			if translate
-				freqs = freqs.map do |term, freq|
-					tr = self.translate_id(term)
-					tr.nil? ? [term, freq] : [tr, freq]
-				end
-			end
-			if asArray
-				freqs = freqs.map{|term, freq| [term, freq]}
-				freqs.sort!{|h1, h2| h2[1] <=> h1[1]}
-			else
-				freqs = freqs.to_h
-			end
-		end
-		return freqs
-	end	
-
-
-	# Clean a given profile returning cleaned set of terms and removed ancestors term.
-	# ===== Parameters
-	# +prof+:: array of terms to be checked
-	# ===== Returns 
-	# two arrays, first is the cleaned profile and second is the removed elements array
-	def remove_ancestors_from_profile(prof)
-		ancestors = prof.map{|term| self.get_ancestors(term)}.flatten.uniq
-		redundant = prof.select{|term| ancestors.include?(term)}
-		return prof - redundant, redundant
-	end
-
-
-	# Remove alternative IDs if official ID is present. DOES NOT REMOVE synonyms or alternative IDs of the same official ID
-	# ===== Parameters
-	# +prof+:: array of terms to be checked
-	# ===== Returns 
-	# two arrays, first is the cleaned profile and second is the removed elements array
-	def remove_alternatives_from_profile(prof)
-		alternatives = prof.select{|term| @alternatives_index.include?(term)}
-		redundant = alternatives.select{|alt_id| prof.include?(@alternatives_index[alt_id])}
-		return prof - redundant, redundant
-	end
-
-
-	# Remove alternatives (if official term is present) and ancestors terms of a given profile 
-	# ===== Parameters
-	# +profile+:: profile to be cleaned
-	# +remove_alternatives+:: if true, clenaed profiles will replace already stored profiles
-	# ===== Returns 
-	# cleaned profile
-	def clean_profile(profile, remove_alternatives: true)
-		terms_without_ancestors, _ = self.remove_ancestors_from_profile(profile)
-		if remove_alternatives
-			terms_without_ancestors_and_alternatices, _ = self.remove_alternatives_from_profile(terms_without_ancestors)
-		else
-			terms_without_ancestors_and_alternatices = terms_without_ancestors
-		end
-		return terms_without_ancestors_and_alternatices
-	end
-
-
-	# Remove alternatives (if official term is present) and ancestors terms of stored profiles 
-	# ===== Parameters
-	# +store+:: if true, clenaed profiles will replace already stored profiles
-	# +remove_alternatives+:: if true, clenaed profiles will replace already stored profiles
-	# ===== Returns 
-	# a hash with cleaned profiles
-	def clean_profiles(store: false, remove_alternatives: true)
-		cleaned_profiles = {}
-		@profiles.each{ |id, terms| cleaned_profiles[id] = self.clean_profile(terms, remove_alternatives: remove_alternatives)}
-		@profiles = cleaned_profiles if store
-		return cleaned_profiles
-	end
-
-
-	# Calculates number of ancestors present (redundant) in each profile stored
-	# ===== Returns 
-	# array of parentals for each profile
-	def parentals_per_profile
-		cleaned_profiles = self.clean_profiles(remove_alternatives: false)
-		parentals = @profiles.map{ |id, terms| terms.length - cleaned_profiles[id].length}
-		return parentals
-	end
-
-
-	#  Calculates mean IC of a given profile
-	# ===== Parameters
-	# +prof+:: profile to be checked
-	# +ic_type+:: ic_type to be used
-	# +zhou_k+:: special coeficient for Zhou IC method
-	# ===== Returns 
-	# mean IC for a given profile
-	def get_profile_mean_IC(prof, ic_type: :resnik, zhou_k: 0.5)
-		return prof.map{|term| self.get_IC(term, type: ic_type, zhou_k: zhou_k)}.inject(0){|sum,x| sum + x}.fdiv(prof.length)
-	end	
-
-
-	# Calculates resnik ontology, and resnik observed mean ICs for all profiles stored
-	# ===== Returns 
-	# two hashes with Profiles and IC calculated for resnik and observed resnik respectively
-	def get_profiles_resnik_dual_ICs
-		struct_ics = {}
-		observ_ics = {}
-		@profiles.each do |id, terms|
-			struct_ics[id] = self.get_profile_mean_IC(terms, ic_type: :resnik)
-			observ_ics[id] = self.get_profile_mean_IC(terms, ic_type: :resnik_observed)
-		end
-		return struct_ics.clone, observ_ics.clone
-	end	
-
-
-	# Calculates ontology structural levels for all ontology terms
-	# ===== Parameters
-	# +calc_paths+:: calculates term paths if it's not already calculated
-	# +shortest_path+:: if true, level is calculated with shortest path, largest path will be used in other cases
-	def calc_term_levels(calc_paths: false, shortest_path: true)
-		if @term_paths.empty?
-			if calc_paths
-				self.calc_term_paths
-			else
-				warn('Term paths are not already loaded. Aborting dictionary calc') 
-			end
-		end
-		if !@term_paths.empty?
-			byTerm = {}
-			byValue = {}
-			# Calc per term
-			@term_paths.each do |term, info|
-				level = shortest_path ? info[:shortest_path] : info[:largest_path]
-				if level.nil?
-					level = -1
-				else
-					level = level.round(0)
-				end
-				byTerm[term] = level
-				queryLevels = byValue[level]
-				if queryLevels.nil?
-					byValue[level] = [term]
-				else
-					byValue[level] << term
-				end
-			end
-			@dicts[:level] = {byTerm: byValue, byValue: byTerm} # Note: in this case, value has multiplicity and term is unique value
-			# Update maximum depth
-			@max_freqs[:max_depth] = byValue.keys.max
-		end
-	end
-
-
-	# Check if a term given is marked as obsolete
-	def is_obsolete? term
-		return @obsoletes_index.include?(term)
-	end
-
-	# Check if a term given is marked as alternative
-	def is_alternative? term
-		return @alternatives_index.include?(term)
-	end
-
-	# Find paths of a term following it ancestors and stores all possible paths for it and it's parentals.
-	# Also calculates paths metadata and stores into @term_paths
-	def calc_term_paths
-		self.calc_ancestors_dictionary if !@dicts.keys.include?(:is_a) # Calculate direct parentals dictionary if it's not already calculated
-		visited_terms = []
-		@term_paths = {}
-		if [:hierarchical, :sparse].include? @structureType
-			terms = @stanzas[:terms].keys
-			terms.each do |term|
-				if self.is_obsolete?(term) || self.is_alternative?(term)  # Special case (obsoletes)
-					special_term = term
-					term = self.is_obsolete?(term) ? @obsoletes_index[term] : @alternatives_index[term]
-					@term_paths[term] = {total_paths: 0, largest_path: 0, shortest_path: 0, paths: []} if !@term_paths.include?(term)
-					@term_paths[special_term] = @term_paths[term]
-					visited_terms << special_term
-				end
-
-				if !visited_terms.include?(term)
-					@term_paths[term] = {total_paths: 0, largest_path: 0, shortest_path: 0, paths: []} if !@term_paths.include?(term)
-					parentals = @dicts[:is_a][:byTerm][term]
-					if parentals.nil?
-						@term_paths[term][:paths] << [term]
-					else
-						parentals.each do |direct_parental|
-							if visited_terms.include? direct_parental # Use direct_parental already calculated paths
-								new_paths = @term_paths[direct_parental][:paths].map{|path| [term, path].flatten}
-							else # Calculate new paths
-								self.expand_path(direct_parental, visited_terms)
-								new_paths = @term_paths[direct_parental][:paths].map{|path| [term, path].flatten}
-							end
-							new_paths.each{|path| @term_paths[term][:paths] << path}
-						end
-					end
-					visited_terms << term
-				end
-				# Update metadata
-				@term_paths[term][:total_paths] = @term_paths[term][:paths].length
-				paths_sizes = @term_paths[term][:paths].map{|path| path.length}
-				@term_paths[term][:largest_path] = paths_sizes.max
-				@term_paths[term][:shortest_path] = paths_sizes.min
-			end
-		else
-			warn('Ontology structure must be hierarchical or sparse to calculate term levels. Aborting paths calculation')
-		end
-	end
-
-
-	# Recursive function whic finds paths of a term following it ancestors and stores all possible paths for it and it's parentals
-	# ===== Parameters
-	# +curr_term+:: current visited term
-	# +visited_terms+:: already expanded terms
-	def expand_path(curr_term, visited_terms)
-		if !visited_terms.include?(curr_term) # Not already expanded
-			@term_paths[curr_term] = {total_paths: 0, largest_path: 0, shortest_path: 0, paths: []} if @term_paths[curr_term].nil?
-			direct_parentals = @dicts[:is_a][:byTerm][curr_term]
-			if direct_parentals.nil? # No parents :: End of recurrence
-				@term_paths[curr_term][:paths] << [curr_term]
-			else # Expand and concat
-				direct_parentals.each do |ancestor|
-					self.expand_path(ancestor,visited_terms) if !visited_terms.include?(ancestor)
-					new_paths = @term_paths[ancestor][:paths].map{|path| [curr_term, path].flatten}
-					new_paths.each{|path| @term_paths[curr_term][:paths] << path}
-				end
-			end
-			visited_terms << curr_term
-		end
-	end
-
-
-	# Gets ontology levels calculated
-	# ===== Returns 
-	# ontology levels calculated
-	def get_ontology_levels
-		return @dicts[:level][:byTerm].clone # By term, in this case, is Key::Level, Value::Terms
-	end
-
-
-	# Gets ontology level of a specific term
-	# ===== Returns 
-	# Term level
-	def get_term_level(term)
-		return @dicts[:level][:byValue][term]
-	end
-
-
-	# Return ontology levels from profile terms
-	# ===== Returns 
-	# hash of term levels (Key: level; Value: array of term IDs)
-	def get_ontology_levels_from_profiles(uniq = true) # TODO: remove uniq and check dependencies
-		profiles_terms = @profiles.values.flatten
-		profiles_terms.uniq! if uniq
-		term_freqs_byProfile = {}
-		profiles_terms.each do |term|
-			query = term_freqs_byProfile[term]
-			if query.nil?
-				term_freqs_byProfile[term] = 1
-			else
-				term_freqs_byProfile[term] += 1
-			end
-		end
-		levels_filtered = @dicts[:level][:byTerm].map{|level, terms| [level,terms.map{|t| profiles_terms.include?(t) ? Array.new(term_freqs_byProfile[t], t) : nil}.flatten.compact]}.select{|level, filteredTerms| !filteredTerms.empty?}.to_h
-		return levels_filtered
-	end
-
-
-	# Calculate profiles dictionary with Key= Term; Value = Profiles
-	def calc_profiles_dictionary
-		if @profiles.empty?
-			warn('Profiles are not already loaded. Aborting dictionary calc')
-		else
-			byTerm = {} # Key: Terms
-			# byValue -- Key: Profile == @profiles
-			@profiles.each do |id, terms|
-				terms.each do |term|
-					if byTerm.include?(term)
-						byTerm[term] << id
-					else
-						byTerm[term] = [id]
-					end
-				end
-			end
-			@profilesDict = byTerm
-		end
-	end
-
-
-	# Gets profiles dictionary calculated
-	# ===== Return
-	# profiles dictionary (clone)
-	def get_terms_linked_profiles
-		return @profilesDict.clone
-	end	
-
-
-	# Get related profiles to a given term
-	# ===== Parameters
-	# +term+:: to be checked
-	# ===== Returns 
-	# profiles which contains given term
-	def get_term_linked_profiles(term)
-		return @profilesDict[term]
-	end
-
-
-	# Gets metainfo table from a set of terms
-	# ===== Parameters
-	# +terms+:: IDs to be expanded
-	# +filter_alternatives+:: flag to be used in get_descendants method
-	# ===== Returns 
-	# an array with triplets [TermID, TermName, DescendantsNames]
-	def get_childs_table(terms, filter_alternatives = false)
-		expanded_terms = []
-		terms.each do |t|
-			expanded_terms << [[t, self.translate_id(t)], self.get_descendants(t, filter_alternatives).map{|child| [child, self.translate_id(child)]}]
-		end
-		return expanded_terms
-	end
-
-
-	# Store specific relations hash given into ITEMS structure
-	# ===== Parameters
-	# +relations+:: to be stored
-	# +remove_old_relations+:: substitute ITEMS structure instead of merge new relations
-	# +expand+:: if true, already stored keys will be updated with the unique union of both sets
-	def load_item_relations_to_terms(relations, remove_old_relations = false, expand = false)
-		@items = {} if remove_old_relations
-		if !relations.select{|term, items| !@stanzas[:terms].include?(term)}.empty?
-			warn('Some terms specified are not stored into this ontology. These not correct terms will be stored too')
-		end
-		if !remove_old_relations
-			if !relations.select{|term, items| @items.include?(term)}.empty? && !expand
-				warn('Some terms given are already stored. Stored version will be replaced')
-			end
-		end
-		if expand
-			relations.each do |k,v|
-				if @items.keys.include?(k)
-					@items[k] = (@items[k] + v).uniq
-				else
-					@items[k] = v
-				end
-			end
-		else
-			@items.merge!(relations)
-		end
-	end	
-
-
-	# Assign a dictionary already calculated as a items set.
-	# ===== Parameters
-	# +dictID+:: dictionary ID to be stored (:byTerm will be used)
-	def set_items_from_dict(dictID, remove_old_relations = false)
-		@items = {} if remove_old_relations
-		if(@dicts.keys.include?(dictID))
-			@items.merge(@dicts[dictID][:byTerm])
-		else
-			warn('Specified ID is not calculated. Dict will not be added as a items set')
-		end
-	end
-
-
-	# This method computes childs similarity and impute items to it parentals. To do that Item keys must be this ontology allowed terms.
-	# Similarity will be calculated by text extact similarity unless an ontology object will be provided. In this case, MICAs will be used
-	# ===== Parameters
-	# +ontology+:: (Optional) ontology object which items given belongs
-	# +minimum_childs+:: minimum of childs needed to infer relations to parental. Default: 2
-	# +clean_profiles+:: if true, clena_profiles ontology method will be used over inferred profiles. Only if an ontology object is provided
-	# ===== Returns
-	# void and update items object
-	def expand_items_to_parentals(ontology: nil, minimum_childs: 2, clean_profiles: true)
-		# Check item keys
-		if @items.empty?
-			warn('Items have been not provided yet')
-			return nil
-		end
-		targetKeys = @items.keys.select{|k| self.exists?(k)}
-		if targetKeys.length == 0
-			warn('Any item key is allowed')
-			return nil
-		elsif targetKeys.length < @items.keys.length
-			warn('Some item keys are not allowed')
-		end
-
-		# Expand to parentals
-		targetKeys << targetKeys.map{|t| self.get_ancestors(t, true)}
-		targetKeys.flatten!
-		targetKeys.uniq!
-
-		# Obtain levels (go from leaves to roots)
-		levels = targetKeys.map{|term| self.get_term_level(term)}
-		levels.compact!
-		levels.uniq!
-		levels.sort!
-		levels.reverse!
-		levels.shift # Leaves are not expandable
-
-		# Expand from leaves to roots
-		levels.map do |lvl|
-			curr_keys = targetKeys.select{|k| self.get_term_level(k) == lvl}
-			curr_keys.map do |term_expand|
-				to_infer = []
-				# Obtain childs
-				childs = self.get_descendants(term_expand,true).select{|t| @items.keys.include?(t)}
-				# Expand
-				if childs.length > 0 && minimum_childs == 1 # Special case
-					to_infer = childs.map{|c| @items[c]}.flatten.compact.uniq
-				elsif childs.length >= minimum_childs
-					to_infer = Hash.new(0)
-					# Compare
-					while childs.length > 1
-						curr_term = childs.shift
-						childs.each do |compare_term|
-							pivot_items = @items[curr_term]
-							compare_items = @items[compare_term]
-							if ontology.nil? # Exact match
-								pivot_items.map do |pitem|
-									if compare_items.include?(pitem)
-										to_infer[pitem] += 2
-									end
-								end
-							else # Find MICAs
-								local_infer = Hash.new(0)
-								pivot_items.map do |pitem|
-									micas = compare_items.map{|citem| ontology.get_MICA(pitem, citem)}
-									maxmica = micas[0]
-									micas.each{|mica| maxmica = mica if mica.last > maxmica.last}
-									local_infer[maxmica.first] += 1
-								end
-								compare_items.map do |citem|
-									micas = pivot_items.map{|pitem| ontology.get_MICA(pitem, citem)}
-									maxmica = micas[0]
-									micas.each{|mica| maxmica = mica if mica.last > maxmica.last}
-									local_infer[maxmica.first] += 1
-								end
-								local_infer.each{|t,freq| to_infer[t] += freq if freq >= 2}
-							end
-						end
-					end
-					# Filter infer
-					to_infer = to_infer.select{|k,v| v >= minimum_childs}
-				end
-				# Infer
-				if to_infer.length > 0
-					@items[term_expand] = [] if @items[term_expand].nil?
-					if to_infer.kind_of?(Array)
-						@items[term_expand] = (@items[term_expand] + to_infer).uniq
-					else
-						@items[term_expand] = (@items[term_expand] + to_infer.keys).uniq
-					end
-					@items[term_expand] = ontology.clean_profile(@items[term_expand]) if clean_profiles && !ontology.nil?
-				elsif !@items.include?(term_expand)
-					targetKeys.delete(term_expand)
-				end
-			end
-		end
-	end
-
-
-
-	# NO IDEA WHAT THIS DOES. DON'T USE THIS METHODS IS NOT CHECKED
-	# ===== Parameters
-	# ++::
-	# ===== Returns
-	# ...
- 	def compute_relations_to_items(external_item_list, mode, thresold)
-		results = []
-		penalized_terms = {}
-		# terms_levels = get_terms_levels(@items_relations.keys)
-		terms_with_items_levels = @items_relations.keys.map{|term| self.get_term_level(term)}.uniq
-		terms_levels = self.get_ontology_levels().select{|k,v| terms_with_items_levels.include?(k)}
-		terms_levels = terms_levels.each{|level,terms| [level, terms.select{|t| @items_relations.keys.include?(t)}] } # Use only items terms. MAYBE IT'S NOT OUR TARGET (line added by fmj)
-		levels = terms_levels.keys.sort
-		levels.reverse_each do |level|
-			terms_levels[level].each do |term|
-				associated_items = @items_relations[term]
-				if mode == :elim 
-					items_to_remove = penalized_terms[term]
-					items_to_remove = [] if items_to_remove.nil?
-					pval = get_fisher_exact_test(
-						external_item_list - items_to_remove, 
-						associated_items - items_to_remove, 
-						((associated_items | external_item_list) - items_to_remove).length
-						)
-					if pval <= thresold
-						parents = get_parents(term) # Save the items for each parent term to remove them later in the fisher test
-						parents.each do |prnt|
-							query = penalized_terms[prnt]
-							if query.nil?
-								penalized_terms[prnt] = @items_relations[term].clone # We need a new array to store the following iterations
-							else
-								query.concat(@items_relations[term])
-							end
-						end
-					end
-				end
-				results << [term, pval]
-			end
-		end
-		return results
-	end
-
-
-	# Check if a given ID is a removable (blacklist) term.
-	# +DEPRECATED+ use is_removable? instead
-	# ===== Parameters
-	# +id+:: to be checked
-	# ===== Returns 
-	# true if given term is a removable (blacklist) term or false in other cases
-	def is_removable(id)
-		warn "[DEPRECATION] `is_removable` is deprecated.  Please use `is_removable?` instead."
-		return @removable_terms.include?(id.to_sym)
-	end
-
-	# Check if a given ID is a removable (blacklist) term
-	# ===== Parameters
-	# +id+:: to be checked
-	# ===== Returns 
-	# true if given term is a removable (blacklist) term or false in other cases
-	def is_removable? id
-		return @removable_terms.include?(id.to_sym)
-	end
-
-	############################################
-	# SPECIAL METHODS
-	#############################################
-	def ==(other)
-    	self.header == other.header &&
-		self.stanzas == other.stanzas &&
-		self.ancestors_index == other.ancestors_index &&
-		self.alternatives_index == other.alternatives_index &&
-		self.obsoletes_index == other.obsoletes_index &&
-		self.structureType == other.structureType &&
-		self.ics == other.ics &&
-		self.meta == other.meta &&
-		self.dicts == other.dicts &&
-		self.profiles == other.profiles &&
-		self.profilesDict == other.profilesDict &&
-		(self.items.keys - other.items.keys).empty? &&
-		self.removable_terms == other.removable_terms &&
-		self.special_tags == other.special_tags &&
-		self.items == other.items &&
-		self.term_paths == other.term_paths &&
-		self.max_freqs == other.max_freqs
+    #########################################################
+    # AUTHOR NOTES
+    #########################################################
+
+    # 1 - Store @profiles as @stanzas[:instances]
+    # 2 - Items values (not keys) are imported as strings, not as symbols (maybe add a flag which indicates if values are, or not, symbols?) 
+
+
+    #############################################
+    # FIELDS
+    #############################################
+    # Handled class variables
+    # => @@basic_tags :: hash with main OBO structure tags
+    # => @@allowed_calcs :: hash with allowed ICs and similaritites calcs
+    # => @@symbolizable_ids :: tags which can be symbolized
+    # => @@tags_with_trailing_modifiers :: tags which can include extra info after specific text modifiers
+    #
+    # Handled object variables
+    # => @header :: file header (if is available)
+    # => @stanzas :: OBO stanzas {:terms,:typedefs,:instances}
+    # => @ancestors_index :: hash of ancestors per each term handled with any structure relationships
+    # => @descendants_index :: hash of descendants per each term handled with any structure relationships
+    # => @alternatives_index :: has of alternative IDs (include alt_id and obsoletes)
+    # => @obsoletes_index :: hash of obsoletes and it's new ids
+    # => @special_tags :: set of special tags to be expanded (:is_a, :obsolete, :alt_id)
+    # => @structureType :: type of ontology structure depending on ancestors relationship. Allowed: {atomic, sparse, circular, hierarchical}
+    # => @ics :: already calculated ICs for handled terms and IC types
+    # => @meta :: meta_information about handled terms like [ancestors, descendants, struct_freq, observed_freq]
+    # => @max_freqs :: maximum freqs found for structural and observed freqs
+    # => @dicts :: bidirectional dictionaries with three levels <key|value>: 1º) <tag|hash2>; 2º) <(:byTerm/:byValue)|hash3>; 3º) dictionary <k|v>
+    # => @profiles :: set of terms assigned to an ID
+    # => @profilesDict :: set of profile IDs assigned to a term
+    # => @items :: hash with items relations to terms
+    # => @removable_terms :: array of terms to not be considered
+    # => @term_paths :: metainfo about parental paths of each term
+
+    @@basic_tags = {ancestors: [:is_a], obsolete: :is_obsolete, alternative: [:alt_id,:replaced_by,:consider]}
+    @@allowed_calcs = {ics: [:resnik, :resnik_observed, :seco, :zhou, :sanchez], sims: [:resnik, :lin, :jiang_conrath]}
+    @@symbolizable_ids = [:id, :alt_id, :replaced_by, :consider]
+    @@tags_with_trailing_modifiers = [:is_a, :union_of, :disjoint_from, :relationship, :subsetdef, :synonymtypedef, :property_value]
+    @@multivalue_tags = [:alt_id, :is_a, :subset, :synonym, :xref, :intersection_of, :union_of, :disjoint_from, :relationship, :replaced_by, :consider, :subsetdef, :synonymtypedef, :property_value, :remark]
+    @@symbolizable_ids.concat(@@tags_with_trailing_modifiers)
+    
+    #############################################
+    # CONSTRUCTOR
+    #############################################
+    
+    # Instantiate a OBO_Handler object
+    # ===== Parameters
+    # +file+:: with info to be loaded (.obo ; .json)
+    # +load_file+:: activate load process automatically (only for .obo)
+    # +removable_terms+: term to be removed from calcs
+    # +build+: flag to launch metainfo calculation
+    def initialize(file: nil, load_file: false, removable_terms: [], build: true)
+        # Initialize object variables
+        @header = nil
+        @stanzas = {terms: {}, typedefs: {}, instances: {}}
+        @ancestors_index = {}
+        @descendants_index = {}
+        @alternatives_index = {}
+        @obsoletes_index = {}
+        @structureType = nil
+        @ics = Hash[@@allowed_calcs[:ics].map{|ictype| [ictype, {}]}]
+        @meta = {}
+        @special_tags = @@basic_tags.clone
+        @max_freqs = {:struct_freq => -1.0, :observed_freq => -1.0, :max_depth => -1.0}
+        @dicts = {}
+        @profiles = {}
+        @profilesDict = {}
+        @items = {}
+        @removable_terms = []
+        @term_paths = {}
+        # Load if proceeds
+        add_removable_terms(removable_terms) if !removable_terms.empty?
+        load(file, build: build) if load_file
+    end
+
+
+    #############################################
+    # CLASS METHODS
+    #############################################
+
+    # Expand a (starting) term using a specific tag and return all extended terms into an array and
+    # the relationship structuture observed (hierarchical or circular). If circular structure is
+    # foumd, extended array will be an unique vector without starting term (no loops).
+    # +Note+: we extremly recomend use get_related_ids_by_tag function instead of it (directly)
+    # ===== Parameters
+    # +start+:: term where start to expand
+    # +terms+:: set to be used to expand
+    # +target_tag+:: tag used to expand
+    # +eexpansion+:: already expanded info
+    # +split_info_char+:: special regex used to split info (if it is necessary)
+    # +split_info_indx+:: special index to take splitted info (if it is necessary)
+    # +alt_ids+:: set of alternative IDs
+    # ===== Returns 
+    # A vector with the observed structure (string) and the array with extended terms.
+    def self.get_related_ids(start_id, terms, target_tag, related_ids = {}, alt_ids = {})
+        # Take start_id term available info and already accumulated info
+        current_associations = related_ids[start_id]
+        current_associations = [] if current_associations.nil? 
+        return [:no_term,[]] if terms[start_id].nil?
+        id_relations = terms[start_id][target_tag]
+        return [:source,[]] if id_relations.nil?
+
+        # Prepare auxiliar variables
+        struct = :hierarchical
+
+        # Study direct extensions
+        id_relations = id_relations.clone
+        while id_relations.length > 0
+            id = id_relations.shift
+            id = alt_ids[id].first if alt_ids.include?(id) # NOTE: if you want to persist current ID instead source ID, re-implement this
+            
+            # Handle
+            if current_associations.include?(id) # Check if already have been included into this expansion
+                struct = :circular 
+            else
+                current_associations << id 
+                if related_ids.include?(id) # Check if current already has been expanded
+                    current_associations = current_associations | related_ids[id]
+                    if current_associations.include?(start_id) # Check circular case
+                        struct = :circular
+                        [id, start_id].each{|repeated| current_associations.delete(repeated)}
+                    end    
+                else # Expand
+                    related_ids[start_id] = current_associations
+                    structExp, current_related_ids = self.get_related_ids(id, terms, target_tag, related_ids, alt_ids) # Expand current
+                    current_associations = current_associations | current_related_ids
+                    struct = :circular if structExp == :circular # Check struct                
+                    if current_associations.include?(start_id) # Check circular case
+                        struct = :circular
+                        current_associations.delete(start_id)
+                    end
+                end
+            end
+        end
+        related_ids[start_id] = current_associations
+
+        return struct, current_associations
+    end
+
+
+    # Expand terms using a specific tag and return all extended terms into an array and
+    # the relationship structuture observed (hierarchical or circular). If circular structure is
+    # foumd, extended array will be an unique vector without starting term (no loops) 
+    # ===== Parameters
+    # +terms+:: set to be used to expand
+    # +target_tag+:: tag used to expand
+    # +split_info_char+:: special regex used to split info (if it is necessary)
+    # +split_info_indx+:: special index to take splitted info (if it is necessary)
+    # +alt_ids+:: set of alternative IDs
+    # +obsoletes+:: integer with the number of obsolete IDs. used to calculate structure type.
+    # ===== Returns 
+    # A vector with the observed structure (string) and the hash with extended terms
+    def self.get_related_ids_by_tag(terms:,target_tag:, alt_ids: {}, obsoletes: 0)
+        # Define structure type
+        structType = :hierarchical
+        related_ids = {}
+        terms.each do |id, tags|
+            # Check if target tag is defined
+            if !tags[target_tag].nil?
+                # Obtain related terms
+                set_structure, _ = self.get_related_ids(id, terms, target_tag, related_ids, alt_ids)
+                # Check structure            
+                structType = :circular if set_structure == :circular
+            end
+        end
+
+        # Check special case
+        structType = :atomic if related_ids.length <= 0
+        structType = :sparse if related_ids.length > 0 && ((terms.length - related_ids.length - obsoletes) >= 2)
+        # Return type and hash with related_ids
+        return structType, related_ids
+    end
+
+
+    # Class method to transform string with <tag : info> into hash structure
+    # ===== Parameters
+    # +attributes+:: array tuples with info to be transformed into hash format
+    # ===== Returns 
+    # Attributes stored into hash structure
+    def self.info2hash(attributes, split_char = " ! ", selected_field = 0)
+        # Load info
+        info_hash = {}
+        # Only TERMS multivalue tags (future add Typedefs and Instance)
+        # multivalue_tags = [:alt_id, :is_a, :subset, :synonym, :xref, :intersection_of, :union_of, :disjoint_from, :relationship, :replaced_by, :consider]
+        attributes.each do |tag, value|
+            # Check
+            raise EncodingError, 'Info element incorrect format' if (tag.nil?) || (value.nil?)
+            # Prepare
+            tag = tag.lstrip.to_sym
+            value.lstrip!
+            value = value.split(split_char)[selected_field].to_sym if @@tags_with_trailing_modifiers.include?(tag)
+            
+            # Store
+            query = info_hash[tag]
+            if !query.nil? # Tag already exists
+                if !query.kind_of?(Array) # Check that tag is multivalue
+                    raise('Attempt to concatenate plain text with another. The tag is not declared as multivalue. [' + tag.to_s + '](' + query + ')')
+                else
+                    query << value    # Add new value to tag
+                end
+            else # New entry
+                if @@multivalue_tags.include?(tag)
+                    info_hash[tag] = [value]
+                else
+                    info_hash[tag] = value
+                end
+            end
+        end
+        self.symbolize_ids(info_hash)
+        return info_hash
+    end
+
+
+    # Class method to load an OBO format file (based on OBO 1.4 format). Specially focused on load
+    # the Header, the Terms, the Typedefs and the Instances.
+    # ===== Parameters
+    # +file+:: OBO file to be loaded
+    # ===== Returns 
+    # Hash with FILE, HEADER and STANZAS info
+    def self.load_obo(file) #TODO: Send to obo_parser class
+        raise("File is not defined") if file.nil?
+        # Data variables
+        header = ''
+        stanzas = {terms: {}, typedefs: {}, instances: {}}
+        # Auxiliar variables
+        infoType = 'Header'
+        currInfo = []
+        stanzas_flags = %w[[Term] [Typedef] [Instance]]
+        # Read file
+        File.open(file).each do |line|
+            line.chomp!
+            next if line.empty?
+            fields = line.split(':', 2)
+            # Check if new instance is found
+            if stanzas_flags.include?(line)
+                header = self.process_entity(header, infoType, stanzas, currInfo)
+                # Update info variables
+                currInfo = []
+                infoType = line.gsub!(/[\[\]]/, '')
+                next
+            end
+            # Concat info
+            currInfo << fields  
+        end
+        # Store last loaded info
+        header = self.process_entity(header, infoType, stanzas, currInfo) if !currInfo.empty?
+
+        # Prepare to return
+        finfo = {:file => file, :name => File.basename(file, File.extname(file))}
+        return finfo, header, stanzas
+    end
+
+
+    # Handle OBO loaded info and stores it into correct container and format
+    # ===== Parameters
+    # +header+:: container
+    # +infoType+:: current ontology item type detected
+    # +stanzas+:: container
+    # +currInfo+:: info to be stored
+    # ===== Returns 
+    # header newly/already stored
+    def self.process_entity(header, infoType, stanzas, currInfo)
+        info = self.info2hash(currInfo)
+        # Store current info
+        if infoType.eql?('Header')
+            header = info
+        else
+            id = info[:id]
+            case infoType
+                when 'Term'
+                    stanzas[:terms][id] = info
+                when 'Typedef'
+                    stanzas[:typedefs][id] = info
+                when 'Instance'
+                    stanzas[:instances][id] = info
+            end
+        end
+        return header
+    end
+
+
+    # Symboliza all values into hashs using symbolizable tags as keys
+    # ===== Parameters
+    # +item_hash+:: hash to be checked
+    def self.symbolize_ids(item_hash)
+        @@symbolizable_ids.each do |tag|
+            query = item_hash[tag] 
+            if !query.nil?
+                if query.kind_of?(Array)
+                    query.map!{|item| item.to_sym}
+                else
+                    item_hash[tag] = query.to_sym if !query.nil?
+                end
+            end
+        end
+    end
+
+
+    #
+    # ===== Parameters
+    # +root+:: main term to expand
+    # +ontology+:: to be cutted
+    # +clone+:: if true, given ontology object will not be mutated
+    # +remove_up+:: if true, stores only the root term given an it descendants. If false, only root ancestors will be stored
+    # ===== Returns
+    # An Ontology object with terms after cut the ontology.
+    def self.mutate(root, ontology, clone: true, remove_up: true)
+        ontology = ontology.clone if clone
+        # Obtain affected IDs
+        descendants = ontology.descendants_index[root]
+        descendants << root # Store itself to do not remove it
+        # Remove unnecesary terms
+        ontology.stanzas[:terms] = ontology.stanzas[:terms].select{|id,v| remove_up ? descendants.include?(id) : !descendants.include?(id)}
+        ontology.ics = Hash[@@allowed_calcs[:ics].map{|ictype| [ictype, {}]}]
+        ontology.max_freqs = {:struct_freq => -1.0, :observed_freq => -1.0, :max_depth => -1.0}
+        ontology.dicts = {}
+        ontology.removable_terms = []
+        ontology.term_paths = {}
+        # Recalculate metadata
+        ontology.build_index
+        ontology.add_observed_terms_from_profiles
+        # Finish
+        return ontology
+    end
+
+
+
+    #############################################
+    # GENERAL METHODS
+    #############################################
+
+    # Include removable terms to current removable terms list
+    # ===== Parameters
+    # +terms+:: terms array to be concatenated
+    def add_removable_terms(terms)
+        terms = terms.map{|term| term.to_sym}
+        @removable_terms.concat(terms)
+    end
+
+
+    # Include removable terms to current removable terms list loading new
+    # terms from a one column plain text file
+    # ===== Parameters
+    # +file+:: to be loaded 
+    def add_removable_terms_from_file(file)
+        File.open(excluded_codes_file).each do |line|
+            line.chomp!
+            @removable_terms << line.to_sym
+        end
+    end
+
+    
+    # Increase observed frequency for a specific term
+    # ===== Parameters
+    # +term+:: term which frequency is going to be increased
+    # +increas+:: frequency rate to be increased. Default = 1
+    # ===== Return
+    # true if process ends without errors, false in other cases
+    def add_observed_term(term:,increase: 1.0)
+        # Check
+        raise ArgumentError, "Term given is NIL" if term.nil?
+        return false unless @stanzas[:terms].include?(term)
+        return false if @removable_terms.include?(term)
+        if @alternatives_index.include?(term)
+            alt_id = @alternatives_index[term]
+            @meta[alt_id] = {:ancestors => -1.0,:descendants => -1.0,:struct_freq => 0.0,:observed_freq => 0.0} if @meta[alt_id].nil?
+            @meta[term] = @meta[alt_id]             
+        end
+        # Check if exists
+        @meta[term] = {:ancestors => -1.0,:descendants => -1.0,:struct_freq => 0.0,:observed_freq => 0.0} if @meta[term].nil?
+        # Add frequency
+        @meta[term][:observed_freq] = 0 if @meta[term][:observed_freq] == -1
+        @meta[term][:observed_freq] += increase
+        # Check maximum frequency
+        @max_freqs[:observed_freq] = @meta[term][:observed_freq] if @max_freqs[:observed_freq] < @meta[term][:observed_freq]  
+        return true
+    end
+
+
+    # Increase the arbitrary frequency of a given term set 
+    # ===== Parameters
+    # +terms+:: set of terms to be updated
+    # +increase+:: amount to be increased
+    # +transform_to_sym+:: if true, transform observed terms to symbols. Default: false
+    # ===== Return
+    # true if process ends without errors and false in other cases
+    def add_observed_terms(terms:, increase: 1.0, transform_to_sym: false)
+        # Check
+        raise ArgumentError, 'Terms array given is NIL' if terms.nil?
+        raise ArgumentError, 'Terms given is not an array' if !terms.is_a? Array
+        # Add observations
+        if transform_to_sym
+            checks = terms.map{|id| self.add_observed_term(term: id.to_sym,increase: increase)}
+        else
+            checks = terms.map{|id| self.add_observed_term(term: id,increase: increase)}
+        end
+        return checks
+    end
+
+
+    # Compare to terms sets 
+    # ===== Parameters
+    # +termsA+:: set to be compared
+    # +termsB+:: set to be compared
+    # +sim_type+:: similitude method to be used. Default: resnik
+    # +ic_type+:: ic type to be used. Default: resnik
+    # +bidirectional+:: calculate bidirectional similitude. Default: false
+    # ===== Return
+    # similitude calculated
+    def compare(termsA, termsB, sim_type: :resnik, ic_type: :resnik, bidirectional: true)
+        # Check
+        raise ArgumentError, "Terms sets given are NIL" if termsA.nil? | termsB.nil?
+        raise ArgumentError, "Set given is empty. Aborting similarity calc" if termsA.empty? | termsB.empty?
+        micasA = []
+        # Compare A -> B
+        termsA.each do |tA|
+            micas = termsB.map{|tB| self.get_similarity(tA, tB, type: sim_type, ic_type: ic_type)}
+            # Remove special cases
+            [false,nil].each do |err_value| micas.delete(err_value) end
+            # Obtain maximum value
+            micasA << micas.max if micas.length > 0
+            micasA << 0 if micas.length <= 0
+        end
+        means_sim = micasA.inject{ |sum, el| sum + el }.to_f / micasA.size
+        # Compare B -> A
+        if bidirectional
+            means_simA = means_sim * micasA.size
+            means_simB = self.compare(termsB, termsA, sim_type: sim_type, ic_type: ic_type, bidirectional: false) * termsB.size
+            means_sim = (means_simA + means_simB) / (termsA.size + termsB.size)
+        end
+        # Return
+        return means_sim
+    end
+
+
+    # Compare internal stored profiles against another set of profiles. If an external set is not provided, internal profiles will be compared with itself 
+    # ===== Parameters
+    # +external_profiles+:: set of external profiles. If nil, internal profiles will be compared with itself
+    # +sim_type+:: similitude method to be used. Default: resnik
+    # +ic_type+:: ic type to be used. Default: resnik
+    # +bidirectional+:: calculate bidirectional similitude. Default: false
+    # ===== Return
+    # Similitudes calculated
+    def compare_profiles(external_profiles: nil, sim_type: :resnik, ic_type: :resnik, bidirectional: true)
+        profiles_similarity = {} #calculate similarity between patients profile
+        profiles_ids = @profiles.keys
+        if external_profiles.nil?
+            comp_ids = profiles_ids
+            comp_profiles = @profiles
+            main_ids = comp_ids
+            main_profiles = comp_profiles
+        else
+            comp_ids = external_profiles.keys
+            comp_profiles = external_profiles
+            main_ids = profiles_ids
+            main_profiles = @profiles
+        end
+        # Compare
+        while !main_ids.empty?
+            curr_id = main_ids.shift
+            current_profile = main_profiles[curr_id]
+            comp_ids.each do |id|
+                profile = comp_profiles[id]
+                value = compare(current_profile, profile, sim_type: sim_type, ic_type: ic_type, bidirectional: bidirectional)
+                query = profiles_similarity[curr_id]
+                if query.nil?
+                  profiles_similarity[curr_id] = {id => value}
+                else
+                  query[id] = value
+                end
+            end    
+        end
+        return profiles_similarity
+    end
+
+
+    # Expand alternative IDs arround all already stored terms
+    # ===== Parameters
+    # +alt_tag+:: tag used to expand alternative IDs
+    # ===== Returns 
+    # true if process ends without errors and false in other cases
+    def get_index_alternatives(alt_tag: @@basic_tags[:alternative][0])
+        # Check input
+        raise('stanzas terms empty')  if @stanzas[:terms].empty?
+        # Take all alternative IDs
+        alt_ids2add = {}
+        @stanzas[:terms].each do |id, tags|
+            alt_ids = tags[alt_tag]
+            if !alt_ids.nil?
+                alt_ids = alt_ids - @removable_terms
+                # Update info
+                alt_ids.each do |alt_term|
+                    @alternatives_index[alt_term] = id
+                    alt_ids2add[alt_term] = @stanzas[:terms][id] if !@stanzas[:terms].include?(alt_term)
+                    @ancestors_index[alt_term] = @ancestors_index[id] if !@ancestors_index[id].nil?
+                end
+            end
+        end
+        @stanzas[:terms].merge!(alt_ids2add)
+    end
+
+
+    # Executes basic expansions of tags (alternatives, obsoletes and parentals) with default values
+    # ===== Returns 
+    # true if eprocess ends without errors and false in other cases
+    def build_index()
+        self.get_index_alternatives
+        self.get_index_obsoletes
+        self.get_index_child_parent_relations
+            @alternatives_index.map{|k,v| @alternatives_index[k] = self.extract_id(v)}
+            @alternatives_index.compact!
+            @obsoletes_index.map{|k,v| @obsoletes_index[k] = self.extract_id(v)}
+            @obsoletes_index.compact!
+            @ancestors_index.map{|k,v| @ancestors_index[k] = v.map{|t| self.extract_id(t)}.compact}
+            @ancestors_index.compact!
+            @descendants_index.map{|k,v| @descendants_index[k] = v.map{|t| self.extract_id(t)}.compact}
+            @descendants_index.compact!
+        self.get_index_frequencies
+        self.calc_dictionary(:name)
+        self.calc_dictionary(:synonym, select_regex: /\"(.*)\"/)
+        self.calc_term_levels(calc_paths: true)
+    end
+
+
+    # Calculates regular frequencies based on ontology structure (using parentals)
+    # ===== Returns 
+    # true if everything end without errors and false in other cases
+    def get_index_frequencies()
+        # Check
+        if @ancestors_index.empty?
+            warn('ancestors_index object is empty') 
+        else
+            # Prepare useful variables
+            alternative_terms = @alternatives_index.keys
+            # Per each term, add frequencies
+            @stanzas[:terms].each do |id, tags|            
+                if @alternatives_index.include?(id)
+                    alt_id = @alternatives_index[id]
+                    query = @meta[alt_id] # Check if exist
+                    if query.nil?
+                        query = {ancestors: 0.0, descendants: 0.0, struct_freq: 0.0, observed_freq: 0.0}
+                        @meta[alt_id] = query 
+                    end 
+                    @meta[id] = query
+                    # Note: alternative terms do not increase structural frequencies
+                else # Official term
+                    query = @meta[id] # Check if exist
+                    if query.nil?
+                        query = {ancestors: 0.0, descendants: 0.0, struct_freq: 0.0, observed_freq: 0.0}
+                        @meta[id] = query 
+                    end
+                    # Store metadata
+                    query[:ancestors] = @ancestors_index.include?(id) ? @ancestors_index[id].count{|anc| !alternative_terms.include?(anc)}.to_f : 0.0
+                    query[:descendants] = @descendants_index.include?(id) ? @descendants_index[id].count{|desc| !alternative_terms.include?(desc)}.to_f : 0.0
+                    query[:struct_freq] = query[:descendants] + 1.0
+                    # Update maximums
+                    @max_freqs[:struct_freq] = query[:struct_freq] if @max_freqs[:struct_freq] < query[:struct_freq]  
+                    @max_freqs[:max_depth] = query[:descendants] if @max_freqs[:max_depth] < query[:descendants]  
+                end
+            end
+        end
+    end
+
+
+    # Expand obsoletes set and link info to their alternative IDs
+    # ===== Parameters
+    # +obs_tags+:: tags to be used to find obsoletes
+    # +alt_tags+:: tags to find alternative IDs (if are available)
+    # +reset_obsoletes+:: flag to indicate if obsoletes set must be reset. Default: true
+    # ===== Returns 
+    # true if process ends without errors and false in other cases
+    def get_index_obsoletes(obs_tag: @@basic_tags[:obsolete], alt_tags: @@basic_tags[:alternative])
+        if @stanzas[:terms].empty?
+            warn('stanzas terms empty')
+        else
+            # Check obsoletes
+            @stanzas[:terms].each do |id, term_tags|
+                next if term_tags.nil?
+                query = term_tags[obs_tag]
+                if !query.nil? && query == 'true' # Obsolete tag presence 
+                    next if !@obsoletes_index[id].nil? # Already stored
+                    # Check if alternative value is available
+                    alt_ids = alt_tags.map{|alt| term_tags[alt]}.compact
+                    if !alt_ids.empty?
+                        alt_id = alt_ids.first.first #FIRST tag, FIRST id 
+                        # Store
+                        @alternatives_index[id] = alt_id
+                        @obsoletes_index[id] = alt_id
+                    end
+                end
+            end
+        end
+    end
+
+
+    # Expand parentals set and link all info to their alternative IDs. Also launch frequencies process
+    # ===== Parameters
+    # +tag+:: tag used to expand parentals
+    # +split_info_char+:: special regex used to split info (if it is necessary)
+    # +split_info_indx+:: special index to take splitted info (if it is necessary)
+    # ===== Returns 
+    # true if process ends without errors and false in other cases
+    def get_index_child_parent_relations(tag: @@basic_tags[:ancestors][0])
+        # Check
+        if @stanzas[:terms].nil?
+            warn('stanzas terms empty')
+        else
+            # Expand
+            structType, parentals = self.class.get_related_ids_by_tag(terms: @stanzas[:terms],
+                                                            target_tag: tag,
+                                                            alt_ids: @alternatives_index,
+                                                            obsoletes: @obsoletes_index.length)
+            # Check
+            raise('Error expanding parentals')  if (structType.nil?) || parentals.nil?
+            # Prepare ancestors structure
+            anc = {}
+            des = {}
+            parentals.each do |id, parents|
+                parents = parents - @removable_terms
+                anc[id] = parents
+                parents.each do |anc_id| # Add descendants
+                    if !des.include?(anc_id)
+                        des[anc_id] = [id]
+                    else 
+                        des[anc_id] << id
+                    end
+                end
+            end
+            # Store alternatives
+            @alternatives_index.each do |id,alt|
+                anc[id] = anc[alt] if anc.include?(alt)
+                des[id] = des[alt] if des.include?(alt)
+            end
+            # Check structure
+            if ![:atomic,:sparse].include? structType
+                structType = structType == :circular ? :circular : :hierarchical
+            end
+            # Store
+            @ancestors_index = anc
+            @descendants_index = des
+            @structureType = structType
+        end
+        # Finish        
+    end
+
+
+    # Find ancestors of a given term
+    # ===== Parameters
+    # +term+:: to be checked
+    # +filter_alternatives+:: if true, remove alternatives from final results
+    # ===== Returns 
+    # an array with all ancestors of given term or false if parents are not available yet
+    def get_ancestors(term, filter_alternatives = false)
+        return self.get_familiar(term, true, filter_alternatives)        
+    end
+
+
+    # Find descendants of a given term
+    # ===== Parameters
+    # +term+:: to be checked
+    # +filter_alternatives+:: if true, remove alternatives from final results
+    # ===== Returns 
+    # an array with all descendants of given term or false if parents are not available yet
+    def get_descendants(term, filter_alternatives = false)
+        return self.get_familiar(term, false, filter_alternatives)        
+    end
+
+
+    # Find ancestors/descendants of a given term
+    # ===== Parameters
+    # +term+:: to be checked
+    # +return_ancestors+:: return ancestors if true or descendants if false
+    # +filter_alternatives+:: if true, remove alternatives from final results
+    # ===== Returns 
+    # an array with all ancestors/descendants of given term or nil if parents are not available yet
+    def get_familiar(term, return_ancestors = true, filter_alternatives = false)
+        # Find into parentals
+        familiars = return_ancestors ? @ancestors_index[term] : @descendants_index[term]        
+        if !familiars.nil?
+            familiars = familiars.clone
+            if filter_alternatives
+                familiars.reject!{|fm| @alternatives_index.include?(fm)}
+            end
+        else
+            familiars = []
+        end
+        return familiars
+    end
+
+
+    # Obtain IC of an specific term
+    # ===== Parameters
+    # +term+:: which IC will be calculated
+    # +type+:: of IC to be calculated. Default: resnik
+    # +force+:: force re-calculate the IC. Do not check if it is already calculated
+    # +zhou_k+:: special coeficient for Zhou IC method
+    # ===== Returns 
+    # the IC calculated
+    def get_IC(termRaw, type: :resnik, force: false, zhou_k: 0.5)
+        term = termRaw.to_sym
+        # Check 
+        raise ArgumentError, "IC type specified (#{type}) is not allowed" if !@@allowed_calcs[:ics].include?(type)
+        # Check if it's already calculated
+        return @ics[type][term] if (@ics[type].include? term) && !force
+        # Calculate
+        ic = - 1
+        case type # https://arxiv.org/ftp/arxiv/papers/1310/1310.8059.pdf  |||  https://sci-hub.st/https://doi.org/10.1016/j.eswa.2012.01.082
+            ###########################################
+            #### STRUCTURE BASED METRICS
+            ###########################################
+            # Shortest path
+            # Weighted Link
+            # Hirst and St-Onge Measure
+            # Wu and Palmer
+            # Slimani
+            # Li
+            # Leacock and Chodorow
+            ###########################################
+            #### INFORMATION CONTENT METRICS
+            ###########################################
+            when :resnik # Resnik P: Using Information Content to Evaluate Semantic Similarity in a Taxonomy
+                # -log(Freq(x) / Max_Freq)
+                ic = -Math.log10(@meta[term][:struct_freq].fdiv(@max_freqs[:struct_freq]))
+            when :resnik_observed 
+                # -log(Freq(x) / Max_Freq)
+                ic = -Math.log10(@meta[term][:observed_freq].fdiv(@max_freqs[:observed_freq]))
+            # Lin
+            # Jiang & Conrath
+
+            ###########################################
+            #### FEATURE-BASED METRICS
+            ###########################################
+            # Tversky
+            # x-similarity
+            # Rodirguez
+
+            ###########################################
+            #### HYBRID METRICS
+            ###########################################
+            when :seco, :zhou # SECO:: An intrinsic information content metric for semantic similarity in WordNet
+                #  1 - ( log(hypo(x) + 1) / log(max_nodes) )
+                ic = 1 - Math.log10(@meta[term][:struct_freq]).fdiv(Math.log10(@stanzas[:terms].length - @alternatives_index.length))
+                if :zhou # New Model of Semantic Similarity Measuring in Wordnet                
+                    # k*(IC_Seco(x)) + (1-k)*(log(depth(x))/log(max_depth))
+                    @ics[:seco][term] = ic # Special store
+                    ic = zhou_k * ic + (1.0 - zhou_k) * (Math.log10(@meta[term][:descendants]).fdiv(Math.log10(@max_freqs[:max_depth])))
+                end
+            when :sanchez # Semantic similarity estimation in the biomedical domain: An ontology-basedinformation-theoretic perspective
+                ic = -Math.log10((@meta[term][:descendants].fdiv(@meta[term][:ancestors]) + 1.0).fdiv(@max_freqs[:max_depth] + 1.0))
+            # Knappe
+        end            
+        @ics[type][term] = ic
+        return ic
+    end
+
+
+    # Calculates and return resnik ICs (by ontology and observed frequency) for observed terms
+    # ===== Returns 
+    # two hashes with resnik and resnik_observed ICs for observed terms
+    def get_observed_ics_by_onto_and_freq
+        # Chech there are observed terms
+        if @profiles.empty?
+            resnik = {}
+            resnik_observed = {}
+        else
+            # Calc ICs for all terms
+            observed_terms = @profiles.values.flatten.uniq
+            observed_terms.each{ |term| get_IC(term)}
+            observed_terms.each{ |term| get_IC(term, type: :resnik_observed)}
+            resnik = @ics[:resnik].select{|k,v| observed_terms.include?(k)}
+            resnik_observed = @ics[:resnik_observed].select{|k,v| observed_terms.include?(k)}
+        end
+        return resnik.clone, resnik_observed.clone
+    end
+
+
+    # Find the IC of the Most Index Content shared Ancestor (MICA) of two given terms
+    # ===== Parameters
+    # +termA+:: term to be cheked
+    # +termB+:: term to be checked
+    # +ic_type+:: IC formula to be used
+    # ===== Returns 
+    # the IC of the MICA(termA,termB)
+    def get_ICMICA(termA, termB, ic_type = :resnik)
+        mica = self.get_MICA(termA, termB, ic_type)
+        return mica.first.nil? ? nil : mica.last
+    end
+
+
+    # Find the Most Index Content shared Ancestor (MICA) of two given terms
+    # ===== Parameters
+    # +termA+:: term to be cheked
+    # +termB+:: term to be checked
+    # +ic_type+:: IC formula to be used
+    # ===== Returns 
+    # the MICA(termA,termB) and it's IC
+    def get_MICA(termA, termB, ic_type = :resnik)
+        termA = @alternatives_index[termA] if @alternatives_index.include?(termA)
+        termB = @alternatives_index[termB] if @alternatives_index.include?(termB)
+        mica = [nil,-1.0]
+        # Special case
+        if termA.eql?(termB)
+            ic = self.get_IC(termA, type: ic_type)
+            mica = [termA, ic]
+        else    
+            # Obtain ancestors (include itselfs too)
+            anc_A = self.get_ancestors(termA) 
+            anc_B = self.get_ancestors(termB)
+
+            if !(anc_A.empty? && anc_B.empty?)
+                anc_A << termA
+                anc_B << termB
+                # Find shared ancestors
+                shared_ancestors = anc_A & anc_B
+                # Find MICA
+                if shared_ancestors.length > 0
+                    shared_ancestors.each do |anc|
+                        ic = self.get_IC(anc, type: ic_type)
+                        # Check
+                        mica = [anc,ic] if ic > mica[1]
+                    end
+                end
+            end
+        end
+        return mica
+    end
+
+
+    # Calculate similarity between two given terms
+    # ===== Parameters
+    # +termsA+:: to be compared
+    # +termsB+:: to be compared
+    # +type+:: similitude formula to be used
+    # +ic_type+:: IC formula to be used
+    # ===== Returns 
+    # the similarity between both sets or false if frequencies are not available yet
+    def get_similarity(termA, termB, type: :resnik, ic_type: :resnik)
+        # Check
+        raise ArgumentError, "SIM type specified (#{type}) is not allowed" if !@@allowed_calcs[:sims].include?(type)
+        sim = nil
+        # Launch comparissons
+        sim_res = get_ICMICA(termA, termB, ic_type)
+        if !sim_res.nil?
+            case type
+                when :resnik
+                    sim = sim_res
+                when :lin
+                    sim = (2.0 * sim_res).fdiv(self.get_IC(termA,type: ic_type) + self.get_IC(termB,type: ic_type))
+                when :jiang_conrath # This is not a similarity, this is a disimilarity (distance)
+                    sim = (self.get_IC(termA, type: ic_type) + self.get_IC(termB, type: ic_type)) - (2.0 * sim_res)
+            end
+        end
+        return sim
+    end
+
+
+    # Method used to load information stored into an OBO file and store it into this object.
+    # If a file is specified by input parameter, current @file value is updated
+    # ===== Parameters
+    # +file+:: optional file to update object stored file
+    def load(file, build: true)
+        _, header, stanzas = self.class.load_obo(file)
+        @header = header
+        @stanzas = stanzas
+        self.remove_removable()
+        # @removable_terms.each{|removableID| @stanzas[:terms].delete(removableID)} if !@removable_terms.empty? # Remove if proceed
+        self.build_index() if build
+    end
+
+    # 
+    def remove_removable()
+        @removable_terms.each{|removableID| @stanzas[:terms].delete(removableID)} if !@removable_terms.empty? # Remove if proceed
+    end
+
+
+    # Exports an OBO_Handler object in json format
+    # ===== Parameters
+    # +file+:: where info will be stored
+    def write(file)
+        # Take object stored info
+        obj_info = {header: @header,
+                    stanzas: @stanzas,
+                    ancestors_index: @ancestors_index,
+                    descendants_index: @descendants_index,
+                    alternatives_index: @alternatives_index,
+                    obsoletes_index: @obsoletes_index,
+                    structureType: @structureType,
+                    ics: @ics,
+                    meta: @meta,
+                    special_tags: @special_tags,
+                    max_freqs: @max_freqs,
+                    dicts: @dicts,
+                    profiles: @profiles,
+                    profilesDict: @profilesDict,
+                    items: @items,
+                    removable_terms: @removable_terms,
+                    term_paths: @term_paths}
+        # Convert to JSON format & write
+        File.open(file, "w") { |f| f.write obj_info.to_json }
+    end
+
+
+    def is_number? string
+          true if Float(string) rescue false
+    end
+
+
+    # Read a JSON file with an OBO_Handler object stored
+    # ===== Parameters
+    # +file+:: with object info
+    # +file+:: if true, calculate indexes. Default: true
+    # ===== Return
+    # OBO_Handler internal fields 
+    def read(file, build: true)
+        # Read file
+        jsonFile = File.open(file)
+        jsonInfo = JSON.parse(jsonFile.read, :symbolize_names => true)
+        # Pre-process (Symbolize some hashs values)
+        jsonInfo[:stanzas][:terms].map{|id,info| self.class.symbolize_ids(info)} # STANZAS
+        jsonInfo[:stanzas][:typedefs].map{|id,info| self.class.symbolize_ids(info)}
+        jsonInfo[:stanzas][:instances].map{|id,info| self.class.symbolize_ids(info)}
+        # Optional
+        jsonInfo[:alternatives_index] = jsonInfo[:alternatives_index].map{|id,value| [id, value.to_sym]}.to_h unless jsonInfo[:alternatives_index].nil?
+        jsonInfo[:ancestors_index].map {|id,family_arr| family_arr.map!{|item| item.to_sym}} unless jsonInfo[:ancestors_index].nil?
+        jsonInfo[:descendants_index].map {|id,family_arr| family_arr.map!{|item| item.to_sym}} unless jsonInfo[:descendants_index].nil?
+        jsonInfo[:obsoletes_index] = jsonInfo[:obsoletes_index].map{|id,value| [id, value.to_sym]}.to_h unless jsonInfo[:obsoletes_index].nil?
+        jsonInfo[:dicts] = jsonInfo[:dicts].each do |flag, dictionaries|
+            next if dictionaries.nil?
+            # Special case: byTerm
+            dictionaries[:byTerm] = dictionaries[:byTerm].map do |term, value| 
+                if !term.to_s.scan(/\A[-+]?[0-9]*\.?[0-9]+\Z/).empty?  # Numeric dictionary
+                    [term.to_s.to_i, value.map{|term| term.to_sym}]
+                elsif value.is_a? Numeric # Numeric dictionary
+                    [term.to_sym, value]
+                elsif value.kind_of?(Array) && flag == :is_a
+                    [term.to_sym, value.map{|v| v.to_sym}]
+                else
+                    [term.to_sym, value]
+                end
+            end
+            dictionaries[:byTerm] = dictionaries[:byTerm].to_h
+            # By value
+            dictionaries[:byValue] = dictionaries[:byValue].map do |value, term| 
+                if value.is_a? Numeric # Numeric dictionary
+                    [value, term.to_sym]
+                elsif term.is_a? Numeric # Numeric dictionary
+                    [value.to_s.to_sym, term]
+                elsif flag == :is_a
+                    [value.to_sym, term.map{|v| v.to_sym}]
+                elsif term.kind_of?(Array)
+                    [value.to_sym, term.map{|t| t.to_sym}]
+                else
+                    [value.to_s, term.to_sym]
+                end
+            end
+            dictionaries[:byValue] = dictionaries[:byValue].to_h
+        end 
+        if !jsonInfo[:profiles].nil?
+            jsonInfo[:profiles].map{|id,terms| terms.map!{|term| term.to_sym}}
+            jsonInfo[:profiles].keys.map{|id| jsonInfo[:profiles][id.to_s.to_i] = jsonInfo[:profiles].delete(id) if self.is_number?(id.to_s)}
+        end
+        jsonInfo[:profilesDict].map{|term,ids| ids.map!{|id| id.to_sym if !id.is_a?(Numeric)}} unless jsonInfo[:profilesDict].nil?
+        jsonInfo[:removable_terms] = jsonInfo[:removable_terms].map{|term| term.to_sym} unless jsonInfo[:removable_terms].nil?
+        jsonInfo[:special_tags] = jsonInfo[:special_tags].each do |k, v|
+            next if v.nil?
+            if v.kind_of?(Array)
+                jsonInfo[:special_tags][k] = v.map{|tag| tag.to_sym}
+            else
+                jsonInfo[:special_tags][k] = v.to_sym
+            end
+        end
+        jsonInfo[:items].each{|k,v| jsonInfo[:items][k] = v.map{|item| item.to_sym}} unless jsonInfo[:items].nil?
+        jsonInfo[:term_paths].each{|term,info| jsonInfo[:term_paths][term][:paths] = info[:paths].map{|path| path.map{|t| t.to_sym}}} unless jsonInfo[:term_paths].nil?
+        
+        # Store info
+        @header = jsonInfo[:header]
+        @stanzas = jsonInfo[:stanzas]
+        @ancestors_index = jsonInfo[:ancestors_index]
+        @descendants_index = jsonInfo[:descendants_index]
+        @alternatives_index = jsonInfo[:alternatives_index]
+        @obsoletes_index = jsonInfo[:obsoletes_index]
+        jsonInfo[:structureType] = jsonInfo[:structureType].to_sym unless jsonInfo[:structureType].nil?
+        @structureType = jsonInfo[:structureType]
+        @ics = jsonInfo[:ics]
+        @meta = jsonInfo[:meta]
+        @special_tags = jsonInfo[:special_tags]
+        @max_freqs = jsonInfo[:max_freqs]
+        @dicts = jsonInfo[:dicts]
+        @profiles = jsonInfo[:profiles]
+        @profilesDict = jsonInfo[:profilesDict]
+        @items = jsonInfo[:items]
+        @removable_terms = jsonInfo[:removable_terms]
+        @term_paths = jsonInfo[:term_paths]
+
+        self.build_index() if build
+    end
+
+
+    # Check if a given ID is stored as term into this object
+    # ===== Parameters
+    # +id+:: to be checked 
+    # ===== Return
+    # True if term is allowed or false in other cases
+    def exists? id
+        return stanzas[:terms].include?(id)
+    end
+
+
+    # This method assumes that a text given contains an allowed ID. And will try to obtain it splitting it
+    # ===== Parameters
+    # +text+:: to be checked 
+    # ===== Return
+    # The correct ID if it can be found or nil in other cases
+    def extract_id(text, splitBy: ' ')
+        if self.exists?(text)
+            return text
+        else
+            splittedText = text.to_s.split(splitBy).first.to_sym
+            return self.exists?(splittedText) ? splittedText : nil
+        end
+    end
+
+
+    # Generate a bidirectinal dictionary set using a specific tag and terms stanzas set
+    # This functions stores calculated dictionary into @dicts field.
+    # This functions stores first value for multivalue tags
+    # This function does not handle synonyms for byValue dictionaries
+    # ===== Parameters
+    # +tag+:: to be used to calculate dictionary
+    # +select_regex+:: gives a regfex that can be used to modify value to be stored
+    # +substitute_alternatives+:: flag used to indicate if alternatives must, or not, be replaced by it official ID
+    # +store_tag+:: flag used to store dictionary. If nil, mandatory tag given will be used
+    # +multiterm+:: if true, byValue will allows multi-term linkage (array)
+    # +self_type_references+:: if true, program assumes that refrences will be between Ontology terms, and it term IDs will be checked
+    # ===== Return
+    # void. And stores calcualted bidirectional dictonary into dictionaries main container
+    def calc_dictionary(tag, select_regex: nil, substitute_alternatives: true, store_tag: nil, multiterm: false, self_type_references: false)
+        tag = tag.to_sym
+        store_tag = tag if store_tag.nil?
+        if @stanzas[:terms].empty?
+            warn('Terms are not already loaded. Aborting dictionary calc') 
+        else
+            byTerm = {}
+            byValue = {}
+            # Calc per term
+            @stanzas[:terms].each do |term, tags|
+                referenceTerm = term
+                if @alternatives_index.include?(term) && substitute_alternatives # Special case
+                    referenceTerm = @alternatives_index[term] if !@obsoletes_index.include?(@alternatives_index[term])
+                end
+                queryTag = tags[tag]
+                if !queryTag.nil?
+                    # Pre-process
+                    if !select_regex.nil?
+                        if queryTag.kind_of?(Array)
+                            queryTag = queryTag.map{|value| value.scan(select_regex).first}
+                            queryTag.flatten!
+                        else
+                            queryTag = queryTag.scan(select_regex).first
+                        end
+                        queryTag.compact!
+                    end
+                    if queryTag.kind_of?(Array) # Store
+                        if !queryTag.empty?
+                            if byTerm.include?(referenceTerm)
+                                byTerm[referenceTerm] = (byTerm[referenceTerm] + queryTag).uniq
+                            else
+                                byTerm[referenceTerm] = queryTag
+                            end
+                            if multiterm
+                                queryTag.each do |value|
+                                    byValue[value] = [] if byValue[value].nil? 
+                                    byValue[value] << referenceTerm
+                                end                                
+                            else
+                                queryTag.each{|value| byValue[value] = referenceTerm}
+                            end
+                        end
+                    else
+                        if byTerm.include?(referenceTerm)
+                            byTerm[referenceTerm] = (byTerm[referenceTerm] + [queryTag]).uniq
+                        else
+                            byTerm[referenceTerm] = [queryTag]
+                        end
+                        if multiterm
+                            byValue[queryTag] = [] if byValue[queryTag].nil?
+                            byValue[queryTag] << referenceTerm
+                        else
+                            byValue[queryTag] = referenceTerm
+                        end
+                    end
+                end
+            end
+            
+            # Check self-references
+            if self_type_references
+                byTerm.map do |term, references|
+                    corrected_references = references.map do |t|
+                        checked = self.extract_id(t)
+                        if checked.nil?
+                            t
+                        else
+                            byValue[checked] = byValue.delete(t) if checked != t && !byValue.keys.include?(checked) # Update in byValue
+                            checked
+                        end
+                    end
+                    byTerm[term] = corrected_references.uniq
+                end
+            end
+
+            # Check order
+            byTerm.map do |term,values|
+                if self.exists?(term)
+                    referenceValue = @stanzas[:terms][term][tag]
+                    if !referenceValue.nil?
+                        if !select_regex.nil?
+                            if referenceValue.kind_of?(Array)
+                                referenceValue = referenceValue.map{|value| value.scan(select_regex).first}
+                                referenceValue.flatten!
+                            else
+                                referenceValue = referenceValue.scan(select_regex).first
+                            end
+                            referenceValue.compact!
+                        end
+                        if self_type_references
+                            if referenceValue.kind_of?(Array)
+                                aux = referenceValue.map{|t| self.extract_id(t)}
+                            else
+                                aux = self.extract_id(referenceValue)
+                            end
+                            referenceValue = aux if !aux.nil?
+                        end
+                        referenceValue = [referenceValue] if !referenceValue.kind_of?(Array)
+                        byTerm[term] = referenceValue + (values - referenceValue)
+                    end
+                end
+            end
+
+            # Store
+            @dicts[store_tag] = {byTerm: byTerm, byValue: byValue}
+        end
+    end
+
+
+    # Calculates :is_a dictionary without alternatives substitution
+    def calc_ancestors_dictionary
+        self.calc_dictionary(:is_a, substitute_alternatives: false, self_type_references: true, multiterm: true)
+    end
+
+
+    # Translate a given value using an already calcualted dictionary
+    # ===== Parameters
+    # +toTranslate+:: value to be translated using dictiontionary
+    # +tag+:: used to generate the dictionary
+    # +byValue+:: boolean flag to indicate if dictionary must be used values as keys or terms as keys. Default: values as keys = true
+    # ===== Return
+    # translation
+    def translate(toTranslate, tag, byValue: true)
+        dict = byValue ? @dicts[tag][:byValue] : @dicts[tag][:byTerm]    
+        toTranslate =  get_main_id(toTranslate) if !byValue
+        return dict[toTranslate]
+    end
+
+
+    # Translate a name given
+    # ===== Parameters
+    # +name+:: to be translated
+    # ===== Return
+    # translated name or nil if it's not stored into this ontology
+    def translate_name(name)
+        term = self.translate(name, :name)
+        term = self.translate(name, :synonym) if term.nil?
+        return term            
+    end
+
+
+    # Translate several names and return translations and a list of names which couldn't be translated
+    # ===== Parameters
+    # +names+:: array to be translated
+    # ===== Return
+    # two arrays with translations and names which couldn't be translated respectively
+    def translate_names(names)
+        translated = []
+        rejected = []
+        names.each do |name|
+            tr = self.translate_name(name)
+            if tr.nil?
+                rejected << name
+            else
+                translated << tr
+            end
+        end
+        return translated, rejected
+    end
+
+
+    # Translates a given ID to it assigned name
+    # ===== Parameters
+    # +id+:: to be translated
+    # ===== Return
+    # main name or nil if it's not included into this ontology
+    def translate_id(id)
+        name = self.translate(id, :name, byValue: false)
+        return name.nil? ? nil : name.first
+    end
+
+
+    # Translates several IDs and returns translations and not allowed IDs list
+    # ===== Parameters
+    # +ids+:: to be translated
+    # ===== Return
+    # two arrays with translations and names which couldn't be translated respectively
+    def translate_ids(ids)
+        translated = []
+        rejected = []
+        ids.each do |term_id|
+            tr = self.translate_id(term_id.to_sym)
+            if !tr.nil?
+                translated << tr
+            else
+                rejected << tr
+            end
+        end
+        return translated, rejected
+    end
+
+
+    # ===== Returns 
+    # the main ID assigned to a given ID. If it's a non alternative/obsolete ID itself will be returned
+    # ===== Parameters
+    # +id+:: to be translated
+    # ===== Return
+    # main ID related to a given ID. Returns nil if given ID is not an allowed ID
+    def get_main_id(id)
+        return nil if !@stanzas[:terms].include? id
+        new_id = id
+        mainID = @alternatives_index[id]
+        new_id = mainID if !mainID.nil? & !@obsoletes_index.include?(mainID)
+        return new_id
+    end
+
+
+    # Check a pull of IDs and return allowed IDs removing which are not official terms on this ontology
+    # ===== Parameters
+    # +ids+:: to be checked
+    # ===== Return
+    # two arrays whit allowed and rejected IDs respectively
+    def check_ids(ids, substitute: true)
+        checked_codes = []
+        rejected_codes = []
+        ids.each do |id|
+            if @stanzas[:terms].include? id
+                if substitute
+                    checked_codes << self.get_main_id(id)
+                else
+                    checked_codes << id
+                end
+            else
+                rejected_codes << id
+            end
+        end
+        return checked_codes, rejected_codes
+    end
+
+
+    # Stores a given profile with an specific ID. If ID is already assigend to a profile, it will be replaced
+    # ===== Parameters
+    # +id+:: assigned to profile
+    # +terms+:: array of terms
+    # +substitute+:: subsstitute flag from check_ids
+    def add_profile(id, terms, substitute: true)
+        warn("Profile assigned to ID (#{id}) is going to be replaced") if @profiles.include? id
+        correct_terms, rejected_terms = self.check_ids(terms, substitute: substitute)
+        if !rejected_terms.empty?
+            warn('Given terms contains erroneus IDs. These IDs will be removed')
+        end
+        if id.is_a? Numeric
+            @profiles[id] = correct_terms              
+        else
+            @profiles[id.to_sym] = correct_terms  
+        end
+    end    
+
+
+    # Method used to store a pull of profiles
+    # ===== Parameters
+    # +profiles+:: array/hash of profiles to be stored. If it's an array, numerical IDs will be assigned starting at 1 
+    # +calc_metadata+:: if true, launch calc_profiles_dictionary process
+    # +reset_stored+:: if true, remove already stored profiles
+    # +substitute+:: subsstitute flag from check_ids
+    def load_profiles(profiles, calc_metadata: true, reset_stored: false, substitute: false)
+        self.reset_profiles if reset_stored
+        # Check
+        if profiles.kind_of?(Array)
+            profiles.each_with_index do |items, i|
+                self.add_profile(i, items.map {|item| item.to_sym}, substitute: substitute)
+            end
+        else # Hash
+            if !profiles.keys.select{|id| @profiles.include?(id)}.empty?
+                warn('Some profiles given are already stored. Stored version will be replaced')
+            end
+            profiles.each{|id, prof| self.add_profile(id, prof, substitute: substitute)}
+        end
+
+        self.add_observed_terms_from_profiles(reset: true)
+
+        if calc_metadata
+            self.calc_profiles_dictionary
+        end
+    end
+
+
+    # Internal method used to remove already stored profiles and restore observed frequencies
+    def reset_profiles
+        # Clean profiles storage
+        @profiles = {}
+        # Reset frequency observed
+        @meta.each{|term,info| info[:observed_freq] = 0}
+        @max_freqs[:observed_freq] = 0
+    end
+
+
+    # ===== Returns 
+    # profiles assigned to a given ID
+    # ===== Parameters
+    # +id+:: profile ID
+    # ===== Return
+    # specific profile or nil if it's not stored
+    def get_profile(id)
+        return @profiles[id]
+    end    
+
+
+    # ===== Returns 
+    # an array of sizes for all stored profiles
+    # ===== Return
+    # array of profile sizes
+    def get_profiles_sizes()
+        return @profiles.map{|id,terms| terms.length}
+    end
+
+
+    # ===== Returns 
+    # mean size of stored profiles
+    # ===== Parameters
+    # +round_digits+:: number of digits to round result. Default: 4
+    # ===== Returns 
+    # mean size of stored profiles
+    def get_profiles_mean_size(round_digits: 4)
+        sizes = self.get_profiles_sizes
+        return sizes.inject(0){|sum, n| sum + n}.fdiv(@profiles.length).round(round_digits)
+    end
+
+
+    # Calculates profiles sizes and returns size assigned to percentile given
+    # ===== Parameters
+    # +perc+:: percentile to be returned
+    # +increasing_sort+:: flag to indicate if sizes order must be increasing. Default: false
+    # ===== Returns 
+    # values assigned to percentile asked
+    def get_profile_length_at_percentile(perc=50, increasing_sort: false)
+        prof_lengths = self.get_profiles_sizes.sort
+        prof_lengths.reverse! if !increasing_sort
+        n_profiles = prof_lengths.length 
+        percentile_index = ((perc * (n_profiles - 1)).fdiv(100) - 0.5).round # Take length which not overpass percentile selected
+        percentile_index = 0 if percentile_index < 0 # Special case (caused by literal calc)
+        return prof_lengths[percentile_index]
+    end
+
+
+    # Translate a given profile to terms names
+    # ===== Parameters
+    # +prof+:: array of terms to be translated
+    # ===== Returns 
+    # array of translated terms. Can include nils if some IDs are not allowed
+    def profile_names(prof)
+        return prof.map{|term| self.translate_id(term)}
+    end
+
+
+    # Trnaslates a bunch of profiles to it sets of term names
+    # ===== Parameters
+    # +profs+:: array of profiles
+    # +asArray+:: flag to indicate if results must be returned as: true => an array of tuples [ProfID, ArrayOdNames] or ; false => hashs of translations
+    # ===== Returns 
+    # translated profiles
+    def translate_profiles_ids(profs = [], asArray: true)
+        profs = @profiles if profs.empty?
+        profs = profs.each_with_index.map{|terms, index| [index, terms]}.to_h if profs.kind_of?(Array)
+        profs_names = profs.map{|id, terms| [id, self.profile_names(terms)]}.to_h
+        return asArray ? profs_names.values : profs_names
+    end
+
+
+    # Includes as "observed_terms" all terms included into stored profiles
+    # ===== Parameters
+    # +reset+:: if true, reset observed freqs alreeady stored befor re-calculate
+    def add_observed_terms_from_profiles(reset: false)
+        @meta.each{|term, freqs| freqs[:observed_freq] = -1} if reset
+        @profiles.each{|id, terms| self.add_observed_terms(terms: terms)}
+    end
+
+
+    # Get a term frequency
+    # ===== Parameters
+    # +term+:: term to be checked
+    # +type+:: type of frequency to be returned. Allowed: [:struct_freq, :observed_freq]
+    # ===== Returns 
+    # frequency of term given or nil if term is not allowed
+    def get_frequency(term, type: :struct_freq)
+        queryFreq = @meta[term]
+        return queryFreq.nil? ? nil : queryFreq[type]        
+    end
+
+
+    # Geys structural frequency of a term given
+    # ===== Parameters
+    # +term+:: to be checked
+    # ===== Returns 
+    # structural frequency of given term or nil if term is not allowed
+    def get_structural_frequency(term)
+        return self.get_frequency(term, type: :struct_freq)
+    end
+
+
+    # Gets observed frequency of a term given
+    # ===== Parameters
+    # +term+:: to be checked
+    # ===== Returns 
+    # observed frequency of given term or nil if term is not allowed
+    def get_observed_frequency(term)
+        return self.get_frequency(term, type: :observed_freq)
+    end
+
+
+    # Calculates frequencies of stored profiles terms
+    # ===== Parameters
+    # +ratio+:: if true, frequencies will be returned as ratios between 0 and 1.
+    # +literal+:: if true, literal terms will be used to calculate frequencies instead translate alternative terms
+    # +asArray+:: used to transform returned structure format from hash of Term-Frequency to an array of tuples [Term, Frequency]
+    # +translate+:: if true, term IDs will be translated to 
+    # ===== Returns 
+    # stored profiles terms frequencies
+    def get_profiles_terms_frequency(ratio: true, literal: true, asArray: true, translate: true)
+        n_profiles = @profiles.length
+        if literal
+            freqs = {}
+            @profiles.each do |id, terms|
+                terms.each do |literalTerm|
+                    if freqs.include?(literalTerm)
+                        freqs[literalTerm] += 1
+                    else
+                        freqs[literalTerm] = 1
+                    end
+                end
+            end
+            if (ratio || translate)
+                aux_keys = freqs.keys
+                aux_keys.each do |term| 
+                    freqs[term] = freqs[term].fdiv(n_profiles) if ratio
+                    if translate
+                        tr = self.translate_id(term)
+                        freqs[tr] = freqs.delete(term) if !tr.nil?
+                    end
+                end
+            end
+            if asArray
+                freqs = freqs.map{|term, freq| [term, freq]}
+                freqs.sort!{|h1, h2| h2[1] <=> h1[1]}
+            end
+        else # Freqs translating alternatives
+            freqs = @meta.select{|id, freqs| freqs[:observed_freq] > 0}.map{|id, freqs| [id, ratio ? freqs[:observed_freq].fdiv(n_profiles) : freqs[:observed_freq]]}
+            freqs = freqs.to_h if !asArray
+            if translate
+                freqs = freqs.map do |term, freq|
+                    tr = self.translate_id(term)
+                    tr.nil? ? [term, freq] : [tr, freq]
+                end
+            end
+            if asArray
+                freqs = freqs.map{|term, freq| [term, freq]}
+                freqs.sort!{|h1, h2| h2[1] <=> h1[1]}
+            else
+                freqs = freqs.to_h
+            end
+        end
+        return freqs
+    end    
+
+
+    # Clean a given profile returning cleaned set of terms and removed ancestors term.
+    # ===== Parameters
+    # +prof+:: array of terms to be checked
+    # ===== Returns 
+    # two arrays, first is the cleaned profile and second is the removed elements array
+    def remove_ancestors_from_profile(prof)
+        ancestors = prof.map{|term| self.get_ancestors(term)}.flatten.uniq
+        redundant = prof.select{|term| ancestors.include?(term)}
+        return prof - redundant, redundant
+    end
+
+
+    # Remove alternative IDs if official ID is present. DOES NOT REMOVE synonyms or alternative IDs of the same official ID
+    # ===== Parameters
+    # +prof+:: array of terms to be checked
+    # ===== Returns 
+    # two arrays, first is the cleaned profile and second is the removed elements array
+    def remove_alternatives_from_profile(prof)
+        alternatives = prof.select{|term| @alternatives_index.include?(term)}
+        redundant = alternatives.select{|alt_id| prof.include?(@alternatives_index[alt_id])}
+        return prof - redundant, redundant
+    end
+
+
+    # Remove alternatives (if official term is present) and ancestors terms of a given profile 
+    # ===== Parameters
+    # +profile+:: profile to be cleaned
+    # +remove_alternatives+:: if true, clenaed profiles will replace already stored profiles
+    # ===== Returns 
+    # cleaned profile
+    def clean_profile(profile, remove_alternatives: true)
+        terms_without_ancestors, _ = self.remove_ancestors_from_profile(profile)
+        if remove_alternatives
+            terms_without_ancestors_and_alternatices, _ = self.remove_alternatives_from_profile(terms_without_ancestors)
+        else
+            terms_without_ancestors_and_alternatices = terms_without_ancestors
+        end
+        return terms_without_ancestors_and_alternatices
+    end
+
+
+    # Remove alternatives (if official term is present) and ancestors terms of stored profiles 
+    # ===== Parameters
+    # +store+:: if true, clenaed profiles will replace already stored profiles
+    # +remove_alternatives+:: if true, clenaed profiles will replace already stored profiles
+    # ===== Returns 
+    # a hash with cleaned profiles
+    def clean_profiles(store: false, remove_alternatives: true)
+        cleaned_profiles = {}
+        @profiles.each{ |id, terms| cleaned_profiles[id] = self.clean_profile(terms, remove_alternatives: remove_alternatives)}
+        @profiles = cleaned_profiles if store
+        return cleaned_profiles
+    end
+
+
+    # Calculates number of ancestors present (redundant) in each profile stored
+    # ===== Returns 
+    # array of parentals for each profile
+    def parentals_per_profile
+        cleaned_profiles = self.clean_profiles(remove_alternatives: false)
+        parentals = @profiles.map{ |id, terms| terms.length - cleaned_profiles[id].length}
+        return parentals
+    end
+
+
+    #  Calculates mean IC of a given profile
+    # ===== Parameters
+    # +prof+:: profile to be checked
+    # +ic_type+:: ic_type to be used
+    # +zhou_k+:: special coeficient for Zhou IC method
+    # ===== Returns 
+    # mean IC for a given profile
+    def get_profile_mean_IC(prof, ic_type: :resnik, zhou_k: 0.5)
+        return prof.map{|term| self.get_IC(term, type: ic_type, zhou_k: zhou_k)}.inject(0){|sum,x| sum + x}.fdiv(prof.length)
+    end    
+
+
+    # Calculates resnik ontology, and resnik observed mean ICs for all profiles stored
+    # ===== Returns 
+    # two hashes with Profiles and IC calculated for resnik and observed resnik respectively
+    def get_profiles_resnik_dual_ICs
+        struct_ics = {}
+        observ_ics = {}
+        @profiles.each do |id, terms|
+            struct_ics[id] = self.get_profile_mean_IC(terms, ic_type: :resnik)
+            observ_ics[id] = self.get_profile_mean_IC(terms, ic_type: :resnik_observed)
+        end
+        return struct_ics.clone, observ_ics.clone
+    end    
+
+
+    # Calculates ontology structural levels for all ontology terms
+    # ===== Parameters
+    # +calc_paths+:: calculates term paths if it's not already calculated
+    # +shortest_path+:: if true, level is calculated with shortest path, largest path will be used in other cases
+    def calc_term_levels(calc_paths: false, shortest_path: true)
+        if @term_paths.empty?
+            if calc_paths
+                self.calc_term_paths
+            else
+                warn('Term paths are not already loaded. Aborting dictionary calc') 
+            end
+        end
+        if !@term_paths.empty?
+            byTerm = {}
+            byValue = {}
+            # Calc per term
+            @term_paths.each do |term, info|
+                level = shortest_path ? info[:shortest_path] : info[:largest_path]
+                if level.nil?
+                    level = -1
+                else
+                    level = level.round(0)
+                end
+                byTerm[term] = level
+                queryLevels = byValue[level]
+                if queryLevels.nil?
+                    byValue[level] = [term]
+                else
+                    byValue[level] << term
+                end
+            end
+            @dicts[:level] = {byTerm: byValue, byValue: byTerm} # Note: in this case, value has multiplicity and term is unique value
+            # Update maximum depth
+            @max_freqs[:max_depth] = byValue.keys.max
+        end
+    end
+
+
+    # Check if a term given is marked as obsolete
+    def is_obsolete? term
+        return @obsoletes_index.include?(term)
+    end
+
+    # Check if a term given is marked as alternative
+    def is_alternative? term
+        return @alternatives_index.include?(term)
+    end
+
+    # Find paths of a term following it ancestors and stores all possible paths for it and it's parentals.
+    # Also calculates paths metadata and stores into @term_paths
+    def calc_term_paths
+        self.calc_ancestors_dictionary if !@dicts.keys.include?(:is_a) # Calculate direct parentals dictionary if it's not already calculated
+        visited_terms = []
+        @term_paths = {}
+        if [:hierarchical, :sparse].include? @structureType
+            terms = @stanzas[:terms].keys
+            terms.each do |term|
+                if self.is_obsolete?(term) || self.is_alternative?(term)  # Special case (obsoletes)
+                    special_term = term
+                    term = self.is_obsolete?(term) ? @obsoletes_index[term] : @alternatives_index[term]
+                    @term_paths[term] = {total_paths: 0, largest_path: 0, shortest_path: 0, paths: []} if !@term_paths.include?(term)
+                    @term_paths[special_term] = @term_paths[term]
+                    visited_terms << special_term
+                end
+
+                if !visited_terms.include?(term)
+                    @term_paths[term] = {total_paths: 0, largest_path: 0, shortest_path: 0, paths: []} if !@term_paths.include?(term)
+                    parentals = @dicts[:is_a][:byTerm][term]
+                    if parentals.nil?
+                        @term_paths[term][:paths] << [term]
+                    else
+                        parentals.each do |direct_parental|
+                            if visited_terms.include? direct_parental # Use direct_parental already calculated paths
+                                new_paths = @term_paths[direct_parental][:paths].map{|path| [term, path].flatten}
+                            else # Calculate new paths
+                                self.expand_path(direct_parental, visited_terms)
+                                new_paths = @term_paths[direct_parental][:paths].map{|path| [term, path].flatten}
+                            end
+                            new_paths.each{|path| @term_paths[term][:paths] << path}
+                        end
+                    end
+                    visited_terms << term
+                end
+                # Update metadata
+                @term_paths[term][:total_paths] = @term_paths[term][:paths].length
+                paths_sizes = @term_paths[term][:paths].map{|path| path.length}
+                @term_paths[term][:largest_path] = paths_sizes.max
+                @term_paths[term][:shortest_path] = paths_sizes.min
+            end
+        else
+            warn('Ontology structure must be hierarchical or sparse to calculate term levels. Aborting paths calculation')
+        end
+    end
+
+
+    # Recursive function whic finds paths of a term following it ancestors and stores all possible paths for it and it's parentals
+    # ===== Parameters
+    # +curr_term+:: current visited term
+    # +visited_terms+:: already expanded terms
+    def expand_path(curr_term, visited_terms)
+        if !visited_terms.include?(curr_term) # Not already expanded
+            @term_paths[curr_term] = {total_paths: 0, largest_path: 0, shortest_path: 0, paths: []} if @term_paths[curr_term].nil?
+            direct_parentals = @dicts[:is_a][:byTerm][curr_term]
+            if direct_parentals.nil? # No parents :: End of recurrence
+                @term_paths[curr_term][:paths] << [curr_term]
+            else # Expand and concat
+                direct_parentals.each do |ancestor|
+                    self.expand_path(ancestor,visited_terms) if !visited_terms.include?(ancestor)
+                    new_paths = @term_paths[ancestor][:paths].map{|path| [curr_term, path].flatten}
+                    new_paths.each{|path| @term_paths[curr_term][:paths] << path}
+                end
+            end
+            visited_terms << curr_term
+        end
+    end
+
+
+    # Gets ontology levels calculated
+    # ===== Returns 
+    # ontology levels calculated
+    def get_ontology_levels
+        return @dicts[:level][:byTerm].clone # By term, in this case, is Key::Level, Value::Terms
+    end
+
+
+    # Gets ontology level of a specific term
+    # ===== Returns 
+    # Term level
+    def get_term_level(term)
+        return @dicts[:level][:byValue][term]
+    end
+
+
+    # Return ontology levels from profile terms
+    # ===== Returns 
+    # hash of term levels (Key: level; Value: array of term IDs)
+    def get_ontology_levels_from_profiles(uniq = true) # TODO: remove uniq and check dependencies
+        profiles_terms = @profiles.values.flatten
+        profiles_terms.uniq! if uniq
+        term_freqs_byProfile = {}
+        profiles_terms.each do |term|
+            query = term_freqs_byProfile[term]
+            if query.nil?
+                term_freqs_byProfile[term] = 1
+            else
+                term_freqs_byProfile[term] += 1
+            end
+        end
+        levels_filtered = @dicts[:level][:byTerm].map{|level, terms| [level,terms.map{|t| profiles_terms.include?(t) ? Array.new(term_freqs_byProfile[t], t) : nil}.flatten.compact]}.select{|level, filteredTerms| !filteredTerms.empty?}.to_h
+        return levels_filtered
+    end
+
+
+    # Calculate profiles dictionary with Key= Term; Value = Profiles
+    def calc_profiles_dictionary
+        if @profiles.empty?
+            warn('Profiles are not already loaded. Aborting dictionary calc')
+        else
+            byTerm = {} # Key: Terms
+            # byValue -- Key: Profile == @profiles
+            @profiles.each do |id, terms|
+                terms.each do |term|
+                    if byTerm.include?(term)
+                        byTerm[term] << id
+                    else
+                        byTerm[term] = [id]
+                    end
+                end
+            end
+            @profilesDict = byTerm
+        end
+    end
+
+
+    # Gets profiles dictionary calculated
+    # ===== Return
+    # profiles dictionary (clone)
+    def get_terms_linked_profiles
+        return @profilesDict.clone
+    end    
+
+
+    # Get related profiles to a given term
+    # ===== Parameters
+    # +term+:: to be checked
+    # ===== Returns 
+    # profiles which contains given term
+    def get_term_linked_profiles(term)
+        return @profilesDict[term]
+    end
+
+
+    # Gets metainfo table from a set of terms
+    # ===== Parameters
+    # +terms+:: IDs to be expanded
+    # +filter_alternatives+:: flag to be used in get_descendants method
+    # ===== Returns 
+    # an array with triplets [TermID, TermName, DescendantsNames]
+    def get_childs_table(terms, filter_alternatives = false)
+        expanded_terms = []
+        terms.each do |t|
+            expanded_terms << [[t, self.translate_id(t)], self.get_descendants(t, filter_alternatives).map{|child| [child, self.translate_id(child)]}]
+        end
+        return expanded_terms
+    end
+
+
+    # Store specific relations hash given into ITEMS structure
+    # ===== Parameters
+    # +relations+:: hash to be stored
+    # +remove_old_relations+:: substitute ITEMS structure instead of merge new relations
+    # +expand+:: if true, already stored keys will be updated with the unique union of both sets
+    def load_item_relations_to_terms(relations, remove_old_relations = false, expand = false)
+        @items = {} if remove_old_relations
+        if !relations.select{|term, items| !@stanzas[:terms].include?(term)}.empty?
+            warn('Some terms specified are not stored into this ontology. These not correct terms will be stored too')
+        end
+        if !remove_old_relations
+            if !relations.select{|term, items| @items.include?(term)}.empty? && !expand
+                warn('Some terms given are already stored. Stored version will be replaced')
+            end
+        end
+        if expand
+            relations.each do |k,v|
+                if @items.keys.include?(k)
+                    @items[k] = (@items[k] + v).uniq
+                else
+                    @items[k] = v
+                end
+            end
+        else
+            @items.merge!(relations)
+        end
+    end    
+
+
+    # Assign a dictionary already calculated as a items set.
+    # ===== Parameters
+    # +dictID+:: dictionary ID to be stored (:byTerm will be used)
+    def set_items_from_dict(dictID, remove_old_relations = false)
+        @items = {} if remove_old_relations
+        if(@dicts.keys.include?(dictID))
+            @items.merge(@dicts[dictID][:byTerm])
+        else
+            warn('Specified ID is not calculated. Dict will not be added as a items set')
+        end
+    end
+
+
+    # This method computes childs similarity and impute items to it parentals. To do that Item keys must be this ontology allowed terms.
+    # Similarity will be calculated by text extact similarity unless an ontology object will be provided. In this case, MICAs will be used
+    # ===== Parameters
+    # +ontology+:: (Optional) ontology object which items given belongs
+    # +minimum_childs+:: minimum of childs needed to infer relations to parental. Default: 2
+    # +clean_profiles+:: if true, clena_profiles ontology method will be used over inferred profiles. Only if an ontology object is provided
+    # ===== Returns
+    # void and update items object
+    def expand_items_to_parentals(ontology: nil, minimum_childs: 2, clean_profiles: true)
+        # Check item keys
+        if @items.empty?
+            warn('Items have been not provided yet')
+            return nil
+        end
+        targetKeys = @items.keys.select{|k| self.exists?(k)}
+        if targetKeys.length == 0
+            warn('Any item key is allowed')
+            return nil
+        elsif targetKeys.length < @items.keys.length
+            warn('Some item keys are not allowed')
+        end
+
+        # Expand to parentals
+        targetKeys << targetKeys.map{|t| self.get_ancestors(t, true)}
+        targetKeys.flatten!
+        targetKeys.uniq!
+
+        # Obtain levels (go from leaves to roots)
+        levels = targetKeys.map{|term| self.get_term_level(term)}
+        levels.compact!
+        levels.uniq!
+        levels.sort!
+        levels.reverse!
+        levels.shift # Leaves are not expandable
+
+        # Expand from leaves to roots
+        levels.map do |lvl|
+            curr_keys = targetKeys.select{|k| self.get_term_level(k) == lvl}
+            curr_keys.map do |term_expand|
+                to_infer = []
+                # Obtain childs
+                childs = self.get_descendants(term_expand,true).select{|t| @items.keys.include?(t)}
+                # Expand
+                if childs.length > 0 && minimum_childs == 1 # Special case
+                    to_infer = childs.map{|c| @items[c]}.flatten.compact.uniq
+                elsif childs.length >= minimum_childs
+                    to_infer = Hash.new(0)
+                    # Compare
+                    while childs.length > 1
+                        curr_term = childs.shift
+                        childs.each do |compare_term|
+                            pivot_items = @items[curr_term]
+                            compare_items = @items[compare_term]
+                            if ontology.nil? # Exact match
+                                pivot_items.map do |pitem|
+                                    if compare_items.include?(pitem)
+                                        to_infer[pitem] += 2
+                                    end
+                                end
+                            else # Find MICAs
+                                local_infer = Hash.new(0)
+                                pivot_items.map do |pitem|
+                                    micas = compare_items.map{|citem| ontology.get_MICA(pitem, citem)}
+                                    maxmica = micas[0]
+                                    micas.each{|mica| maxmica = mica if mica.last > maxmica.last}
+                                    local_infer[maxmica.first] += 1
+                                end
+                                compare_items.map do |citem|
+                                    micas = pivot_items.map{|pitem| ontology.get_MICA(pitem, citem)}
+                                    maxmica = micas[0]
+                                    micas.each{|mica| maxmica = mica if mica.last > maxmica.last}
+                                    local_infer[maxmica.first] += 1
+                                end
+                                local_infer.each{|t,freq| to_infer[t] += freq if freq >= 2}
+                            end
+                        end
+                    end
+                    # Filter infer
+                    to_infer = to_infer.select{|k,v| v >= minimum_childs}
+                end
+                # Infer
+                if to_infer.length > 0
+                    @items[term_expand] = [] if @items[term_expand].nil?
+                    if to_infer.kind_of?(Array)
+                        @items[term_expand] = (@items[term_expand] + to_infer).uniq
+                    else
+                        @items[term_expand] = (@items[term_expand] + to_infer.keys).uniq
+                    end
+                    @items[term_expand] = ontology.clean_profile(@items[term_expand]) if clean_profiles && !ontology.nil?
+                elsif !@items.include?(term_expand)
+                    targetKeys.delete(term_expand)
+                end
+            end
+        end
+    end
+
+
+
+    # NO IDEA WHAT THIS DOES. DON'T USE THIS METHODS IS NOT CHECKED
+    # ===== Parameters
+    # ++::
+    # ===== Returns
+    # ...
+     def compute_relations_to_items(external_item_list, mode, thresold)
+        results = []
+        penalized_terms = {}
+        # terms_levels = get_terms_levels(@items_relations.keys)
+        terms_with_items_levels = @items_relations.keys.map{|term| self.get_term_level(term)}.uniq
+        terms_levels = self.get_ontology_levels().select{|k,v| terms_with_items_levels.include?(k)}
+        terms_levels = terms_levels.each{|level,terms| [level, terms.select{|t| @items_relations.keys.include?(t)}] } # Use only items terms. MAYBE IT'S NOT OUR TARGET (line added by fmj)
+        levels = terms_levels.keys.sort
+        levels.reverse_each do |level|
+            terms_levels[level].each do |term|
+                associated_items = @items_relations[term]
+                if mode == :elim 
+                    items_to_remove = penalized_terms[term]
+                    items_to_remove = [] if items_to_remove.nil?
+                    pval = get_fisher_exact_test(
+                        external_item_list - items_to_remove, 
+                        associated_items - items_to_remove, 
+                        ((associated_items | external_item_list) - items_to_remove).length
+                        )
+                    if pval <= thresold
+                        parents = get_parents(term) # Save the items for each parent term to remove them later in the fisher test
+                        parents.each do |prnt|
+                            query = penalized_terms[prnt]
+                            if query.nil?
+                                penalized_terms[prnt] = @items_relations[term].clone # We need a new array to store the following iterations
+                            else
+                                query.concat(@items_relations[term])
+                            end
+                        end
+                    end
+                end
+                results << [term, pval]
+            end
+        end
+        return results
+    end
+
+
+    # Check if a given ID is a removable (blacklist) term.
+    # +DEPRECATED+ use is_removable? instead
+    # ===== Parameters
+    # +id+:: to be checked
+    # ===== Returns 
+    # true if given term is a removable (blacklist) term or false in other cases
+    def is_removable(id)
+        warn "[DEPRECATION] `is_removable` is deprecated.  Please use `is_removable?` instead."
+        return @removable_terms.include?(id.to_sym)
+    end
+
+    # Check if a given ID is a removable (blacklist) term
+    # ===== Parameters
+    # +id+:: to be checked
+    # ===== Returns 
+    # true if given term is a removable (blacklist) term or false in other cases
+    def is_removable? id
+        return @removable_terms.include?(id.to_sym)
+    end
+
+    ############################################
+    # SPECIAL METHODS
+    #############################################
+    def ==(other)
+        self.header == other.header &&
+        self.stanzas == other.stanzas &&
+        self.ancestors_index == other.ancestors_index &&
+        self.alternatives_index == other.alternatives_index &&
+        self.obsoletes_index == other.obsoletes_index &&
+        self.structureType == other.structureType &&
+        self.ics == other.ics &&
+        self.meta == other.meta &&
+        self.dicts == other.dicts &&
+        self.profiles == other.profiles &&
+        self.profilesDict == other.profilesDict &&
+        (self.items.keys - other.items.keys).empty? &&
+        self.removable_terms == other.removable_terms &&
+        self.special_tags == other.special_tags &&
+        self.items == other.items &&
+        self.term_paths == other.term_paths &&
+        self.max_freqs == other.max_freqs
     end
 
 
     def clone
-    	copy = Ontology.new
-    	copy.header = self.header.clone
-		copy.stanzas[:terms] = self.stanzas[:terms].clone
-		copy.stanzas[:typedefs] = self.stanzas[:typedefs].clone
-		copy.stanzas[:instances] = self.stanzas[:instances].clone
-		copy.ancestors_index = self.ancestors_index.clone
-		copy.descendants_index = self.descendants_index.clone
-		copy.alternatives_index = self.alternatives_index.clone
-		copy.obsoletes_index = self.obsoletes_index.clone
-		copy.structureType = self.structureType.clone
-		copy.ics = self.ics.clone
-		copy.meta = self.meta.clone
-		copy.dicts = self.dicts.clone
-		copy.profiles = self.profiles.clone
-		copy.profilesDict = self.profilesDict.clone
-		copy.items = self.items.clone
-		copy.removable_terms = self.removable_terms.clone
-		copy.term_paths = self.term_paths.clone
-		copy.max_freqs = self.max_freqs.clone
-		return copy
-    end
-
-	
-	#############################################
-	# ACCESS CONTROL
-	#############################################
-
-	attr_reader :file, :header, :stanzas, :ancestors_index, :descendants_index, :special_tags, :alternatives_index, :obsoletes_index, :structureType, :ics, :max_freqs, :meta, :dicts, :profiles, :profilesDict, :items, :removable_terms, :term_paths
-	attr_writer :file, :header, :stanzas, :ancestors_index, :descendants_index, :special_tags, :alternatives_index, :obsoletes_index, :structureType, :ics, :max_freqs, :meta, :dicts, :profiles, :profilesDict, :items, :removable_terms, :term_paths
+        copy = Ontology.new
+        copy.header = self.header.clone
+        copy.stanzas[:terms] = self.stanzas[:terms].clone
+        copy.stanzas[:typedefs] = self.stanzas[:typedefs].clone
+        copy.stanzas[:instances] = self.stanzas[:instances].clone
+        copy.ancestors_index = self.ancestors_index.clone
+        copy.descendants_index = self.descendants_index.clone
+        copy.alternatives_index = self.alternatives_index.clone
+        copy.obsoletes_index = self.obsoletes_index.clone
+        copy.structureType = self.structureType.clone
+        copy.ics = self.ics.clone
+        copy.meta = self.meta.clone
+        copy.dicts = self.dicts.clone
+        copy.profiles = self.profiles.clone
+        copy.profilesDict = self.profilesDict.clone
+        copy.items = self.items.clone
+        copy.removable_terms = self.removable_terms.clone
+        copy.term_paths = self.term_paths.clone
+        copy.max_freqs = self.max_freqs.clone
+        return copy
+    end
+
+    
+    #############################################
+    # ACCESS CONTROL
+    #############################################
+
+    attr_reader :file, :header, :stanzas, :ancestors_index, :descendants_index, :special_tags, :alternatives_index, :obsoletes_index, :structureType, :ics, :max_freqs, :meta, :dicts, :profiles, :profilesDict, :items, :removable_terms, :term_paths
+    attr_writer :file, :header, :stanzas, :ancestors_index, :descendants_index, :special_tags, :alternatives_index, :obsoletes_index, :structureType, :ics, :max_freqs, :meta, :dicts, :profiles, :profilesDict, :items, :removable_terms, :term_paths
 end