Module: Bio::NCBI::REST::ESearch::Methods

Included in:
Bio::NCBI::REST::ESearch, Bio::NCBI::REST::ESearch
Defined in:
lib/bio/io/ncbirest.rb

Overview

Search database entries by given keywords using E-Utils (esearch).

sequences = gene + genome + nucleotide + protein + popset + snp
nucleotide = nuccore + nucest + nucgss

pubmed protein nucleotide nuccore nucgss nucest structure genome
books cancerchromosomes cdd gap domains gene genomeprj gensat geo
gds homologene journals mesh ncbisearch nlmcatalog omia omim pmc
popset probe proteinclusters pcassay pccompound pcsubstance snp
taxonomy toolkit unigene unists

Usage

Bio::NCBI::REST::ESearch.search("nucleotide", "tardigrada")
Bio::NCBI::REST::ESearch.count("nucleotide", "tardigrada")

Bio::NCBI::REST::ESearch.nucleotide("tardigrada")
Bio::NCBI::REST::ESearch.popset("aldh2")
Bio::NCBI::REST::ESearch.taxonomy("tardigrada")
Bio::NCBI::REST::ESearch.pubmed("tardigrada", "reldate" => 365)
Bio::NCBI::REST::ESearch.pubmed("mammoth mitochondrial genome")
Bio::NCBI::REST::ESearch.pmc("Indonesian coelacanth genome Latimeria menadoensis")
Bio::NCBI::REST::ESearch.journal("bmc bioinformatics")

ncbi = Bio::NCBI::REST::ESearch.new
ncbi.search("nucleotide", "tardigrada")
ncbi.count("nucleotide", "tardigrada")

ncbi.nucleotide("tardigrada")
ncbi.popset("aldh2")
ncbi.taxonomy("tardigrada")
ncbi.pubmed("tardigrada", "reldate" => 365)
ncbi.pubmed("mammoth mitochondrial genome")
ncbi.pmc("Indonesian coelacanth genome Latimeria menadoensis")
ncbi.journal("bmc bioinformatics")

Arguments:

  • term: search keywords (required)

  • limit: maximum number of entries to be returned (0 for unlimited)

  • hash: hash of E-Utils option

Returns

array of entry IDs or a number of results

Instance Method Summary collapse

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(*args) ⇒ Object

nucleotide(“tardigrada”) nucleotide(“tardigrada”, 0) pubmed(“tardigrada”) pubmed(“tardigrada”, 5) pubmed(“tardigrada”, “reldate” => 365) pubmed(“tardigrada”, 5, “reldate” => 365) pubmed(“tardigrada”, => 365, 5)



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# File 'lib/bio/io/ncbirest.rb', line 449

def method_missing(*args)
  self.search(*args)
end

Instance Method Details

#count(db, term, hash = {}) ⇒ Object

count(“nucleotide”, “tardigrada”) count(“pubmed”, “tardigrada”) count(“journals”, “bmc”)



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# File 'lib/bio/io/ncbirest.rb', line 436

def count(db, term, hash = {})
  opts = { "db" => db }
  opts.update(hash)
  Bio::NCBI::REST.esearch_count(term, opts)
end

#est(*args) ⇒ Object

alias for “nucest”



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# File 'lib/bio/io/ncbirest.rb', line 459

def est(*args)
  self.search("nucest", *args)
end

#gss(*args) ⇒ Object

alias for “nucgss”



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# File 'lib/bio/io/ncbirest.rb', line 464

def gss(*args)
  self.search("nucgss", *args)
end

#journal(*args) ⇒ Object

alias for journals



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# File 'lib/bio/io/ncbirest.rb', line 454

def journal(*args)
  self.search("journals", *args)
end

#search(db, term, *args) ⇒ Object

search(“nucleotide”, “tardigrada”) search(“nucleotide”, “tardigrada”, 0) # unlimited search(“pubmed”, “tardigrada”) search(“pubmed”, “tardigrada”, 5) # first five search(“pubmed”, “tardigrada”, “reldate” => 365) # within a year search(“pubmed”, “tardigrada”, 5, “reldate” => 365) # combination search(“pubmed”, “tardigrada”, => 365, 5) # combination 2 search(“journals”, “bmc”, 10)



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# File 'lib/bio/io/ncbirest.rb', line 417

def search(db, term, *args)
  limit = 100
  hash = {}
  args.each do |arg|
    case arg
    when Hash
      hash.update(arg)
    else
      limit = arg.to_i
    end
  end
  opts = { "db" => db }
  opts.update(hash)
  Bio::NCBI::REST.esearch(term, opts, limit)
end