module Phenoscape::Studies
Public Class Methods
Return a data matrix in NeXML format containing the data for a given study.
@!macro phenoscape_params @!macro phenoscape_options @param iri [String] the study IRI @return [Hash] A hash
@example
require 'phenoscaperb' tax = Phenoscape::Studies st.matrix(iri: "http://www.pfeilbook.com/07pala/pdf/2_48d15.pdf")
# File lib/phenoscaperb/Studies.rb, line 94 def self.matrix(iri:, ret: "hash", verbose: nil, options: nil) arguments = { iri: iri }.tostrings opts = arguments.delete_if { |k, v| v.nil? } Request.new("study/matrix", opts, verbose, options, ret, "text/plain").perform end
Character states and their phenotypes annotated within a study
@!macro phenoscape_params @!macro phenoscape_options @param iri [String] the study IRI @param limit [Integer] maximum results to return @param offset [Integer] index of results to begin returning @param total [boolean] whether to return the total result count rather than the results @return [Hash] A hash
@example
require 'phenoscaperb' tax = Phenoscape::Studies st.phenotypes(iri: "http://www.pfeilbook.com/07pala/pdf/2_48d15.pdf")
# File lib/phenoscaperb/Studies.rb, line 75 def self.phenotypes(iri:, limit: 20, offset: 0, total: false, verbose: nil, options: nil) arguments = { iri: iri, limit: limit, offset: offset, total: total }.tostrings opts = arguments.delete_if { |k, v| v.nil? } Request.new("study/phenotypes", opts, verbose, options, nil).perform end
Return studies containing taxa which are members of the optional input taxon expression and are have annotated phenotypes which are relevant to the optional input entity expression.
@!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 @return [Hash] A hash
@example
require 'phenoscaperb' st = Phenoscape::Studies st.query(taxon: "<http://purl.obolibrary.org/obo/VTO_0037519>", entity: "<http://purl.obolibrary.org/obo/UBERON_0001703>")
# File lib/phenoscaperb/Studies.rb, line 31 def self.query(taxon:, entity:, verbose: nil, options: nil) arguments = { taxon: taxon, entity: entity }.tostrings opts = arguments.delete_if { |k, v| v.nil? } Request.new("study/query", opts, verbose, options, nil).perform end
Taxa
annotated within a study
@!macro phenoscape_params @!macro phenoscape_options @param iri [String] the study IRI @param limit [Integer] maximum results to return @param offset [Integer] index of results to begin returning @param total [boolean] whether to return the total result count rather than the results @return [Hash] A hash
@example
require 'phenoscaperb' tax = Phenoscape::Studies st.taxa(iri: "http://www.pfeilbook.com/07pala/pdf/2_48d15.pdf")
# File lib/phenoscaperb/Studies.rb, line 53 def self.taxa(iri:, limit: 20, offset: 0, total: false, verbose: nil, options: nil) arguments = { iri: iri, limit: limit, offset: offset, total: total }.tostrings opts = arguments.delete_if { |k, v| v.nil? } Request.new("study/taxa", opts, verbose, options, nil).perform end