module Phenoscape::Studies

Public Class Methods

matrix(iri:, ret: "hash", verbose: nil, options: nil) click to toggle source

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
phenotypes(iri:, limit: 20, offset: 0, total: false, verbose: nil, options: nil) click to toggle source

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
query(taxon:, entity:, verbose: nil, options: nil) click to toggle source

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(iri:, limit: 20, offset: 0, total: false, verbose: nil, options: nil) click to toggle source

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