module Phenoscape::Taxa

Public Class Methods

annotations(entity: nil, quality: nil, in_taxon: nil, parts: false, historical_homologs: false, serial_homologs: false, limit: 20, offset: 0, total: false, verbose: nil, options: nil) click to toggle source

Retrieve taxa annotations

@!macro phenoscape_params @!macro phenoscape_options @param entity [String] Anatomical class expression @param quality [String] Quality class expression @param in_taxon [String] A taxon group to limit the results @param parts [boolean] whether to include phenotypes of parts of the entity. default: false @param historical_homologs [boolean] whether to include historical homologs of the entity in the query. default: false @param serial_homologs [boolean] whether to include serial homologs of the entity in the query. default: false @param total [boolean] whether to return the total result count rather than the results. default: false @return [Hash] A hash

@example

require 'phenoscaperb'

tax = Phenoscape::Taxa
tax.annotations(entity: "http://purl.obolibrary.org/obo/UBERON_0001703", quality: "http://purl.obolibrary.org/obo/PATO_0000052", in_taxon: "http://purl.obolibrary.org/obo/VTO_0037519", parts: true, historical_homologs: false, serial_homologs: false, limit: 20, offset: 0, total: true)
# File lib/phenoscaperb/Taxa.rb, line 104
def self.annotations(entity: nil, quality: nil, in_taxon: nil, parts: false, historical_homologs: false,
    serial_homologs: false, limit: 20, offset: 0, total: false, verbose: nil, options: nil)

  arguments = { entity: entity, quality: quality, in_taxon: in_taxon, parts: parts, 
    historical_homologs: historical_homologs, serial_homologs: serial_homologs, 
    limit: limit, offset: offset, total: total }.tostrings
  opts = arguments.delete_if { |k, v| v.nil? }
  Request.new("taxon/annotations", opts, verbose, options, nil).perform
end
taxon(iri:, verbose: nil, options: nil) click to toggle source

Return detail info for a given taxon. Currently this is the label, extinction status, and an optional rank.

@!macro phenoscape_params @!macro phenoscape_options @param iri [String] a taxon IRI @return [Hash] A hash

@example

require 'phenoscaperb'

tax = Phenoscape::Taxa
tax.taxon(iri: "http://purl.obolibrary.org/obo/VTO_0067193")
# File lib/phenoscaperb/Taxa.rb, line 30
def self.taxon(iri:, verbose: nil, options: nil)

  arguments = { iri: iri }.tostrings
  opts = arguments.delete_if { |k, v| v.nil? }
  Request.new("taxon", opts, verbose, options, nil).perform
end
taxon_with_rank(rank:, in_taxon:, verbose: nil, options: nil) click to toggle source

Retrieve all taxa with a given taxonomic rank, within the given super-taxon. Ranks are term IRIs from the taxonomic rank ontology such as order, family, genus, species.

@!macro phenoscape_params @!macro phenoscape_options @param rank [String] a rank IRI @param in_taxon [String] a taxon IRI @return [Hash] A hash

@example

require 'phenoscaperb'

tax = Phenoscape::Taxa
tax.taxon_with_rank(rank: "http://purl.obolibrary.org/obo/TAXRANK_0000003", in_taxon: "http://purl.obolibrary.org/obo/VTO_0000009")
# File lib/phenoscaperb/Taxa.rb, line 50
def self.taxon_with_rank(rank:, in_taxon:, verbose: nil, options: nil)

  arguments = { rank: rank, in_taxon: in_taxon }.tostrings
  opts = arguments.delete_if { |k, v| v.nil? }
  Request.new("taxon/with_rank", opts, verbose, options, nil).perform
end
with_phenotype(entity: nil, quality: nil, in_taxon: nil, parts: false, historical_homologs: false, serial_homologs: false, limit: 20, offset: 0, total: false, verbose: nil, options: nil) click to toggle source

Retrieve taxa with annotated phenotypes related to the given anatomical entity or quality.

@!macro phenoscape_params @!macro phenoscape_options @param entity [String] Anatomical class expression in OWL Manchester syntax @param quality [String] Quality class expression in OWL Manchester syntax @param in_taxon [String] A taxon group to limit the results @param parts [boolean] whether to include phenotypes of parts of the entity. default: false @param historical_homologs [boolean] whether to include historical homologs of the entity in the query. default: false @param serial_homologs [boolean] whether to include serial homologs of the entity in the query. default: false @param total [boolean] whether to return the total result count rather than the results. default: false @return [Hash] A hash

@example

require 'phenoscaperb'

tax = Phenoscape::Taxa
tax.with_phenotype(entity: "<http://purl.obolibrary.org/obo/UBERON_0008897>", quality: "<http://purl.obolibrary.org/obo/PATO_0000052>", in_taxon: "http://purl.obolibrary.org/obo/VTO_0059975")
tax.with_phenotype(entity: "<http://purl.obolibrary.org/obo/UBERON_0008897>", quality: "<http://purl.obolibrary.org/obo/PATO_0000052>", in_taxon: "http://purl.obolibrary.org/obo/VTO_0059975", total: true)
# File lib/phenoscaperb/Taxa.rb, line 76
def self.with_phenotype(entity: nil, quality: nil, in_taxon: nil, parts: false, historical_homologs: false,
    serial_homologs: false, limit: 20, offset: 0, total: false, verbose: nil, options: nil)

  arguments = { entity: entity, quality: quality, in_taxon: in_taxon, parts: parts, 
    historical_homologs: historical_homologs, serial_homologs: serial_homologs, 
    limit: limit, offset: offset, total: total }.tostrings
  opts = arguments.delete_if { |k, v| v.nil? }
  Request.new("taxon/with_phenotype", opts, verbose, options, nil).perform
end