module Phenoscape::Ontotrace
Public Class Methods
ontotrace(taxon:, entity:, variable_only: nil, ret: "hash", verbose: nil, options: nil)
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Generate matrix of inferred presence/absence associations for anatomical structures subsumed by the provided entity class expression, for any taxa within the provided taxon class expression. Returns a NeXML-format evolutionary character matrix. @!macro phenoscape_params @!macro phenoscape_options @param taxon [String] Taxonomic class expression in OWL Manchester syntax @param entity [String] Anatomical class expression in OWL Manchester syntax @param variable_only [boolean] whether to restrict the matrix to characters with both ‘present’ and ‘absent’ values in the matrix. default: true @param ret [String] what to return, one of hash (default), text (raw xml [nexml] as text), or noko (class 'Nokogiri::XML::Document') @return [Hash] A hash @example require 'phenoscaperb' onto = Phenoscape::Ontotrace onto.ontotrace(taxon: "<http://purl.obolibrary.org/obo/VTO_0058051>", entity: "<http://purl.obolibrary.org/obo/BFO_0000050>") onto.ontotrace(taxon: "<http://purl.obolibrary.org/obo/VTO_0058051>", entity: "<http://purl.obolibrary.org/obo/BFO_0000050>", variable_only: false)
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. # this one times out
# onto.ontotrace(taxon: "http://purl.obolibrary.org/obo/VTO_0033622", entity: "http://purl.obolibrary.org/obo/UBERON_0003097")
# File lib/phenoscaperb/Ontotrace.rb, line 38 def self.ontotrace(taxon:, entity:, variable_only: nil, ret: "hash", verbose: nil, options: nil) arguments = { taxon: taxon, entity: entity, variable_only: variable_only }.tostrings opts = arguments.delete_if { |k, v| v.nil? } Request.new("ontotrace", opts, verbose, options, ret, "application/xml").perform end