module Bio::NCBI::REST::ESearch::Methods

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:

Returns

array of entry IDs or a number of results

Public Instance Methods

count(db, term, hash = {}) click to toggle source

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

    # File lib/bio/io/ncbirest.rb
475 def count(db, term, hash = {})
476   opts = { "db" => db }
477   opts.update(hash)
478   Bio::NCBI::REST.esearch_count(term, opts)
479 end
est(*args) click to toggle source

alias for “nucest”

    # File lib/bio/io/ncbirest.rb
498 def est(*args)
499   self.search("nucest", *args)
500 end
gss(*args) click to toggle source

alias for “nucgss”

    # File lib/bio/io/ncbirest.rb
503 def gss(*args)
504   self.search("nucgss", *args)
505 end
journal(*args) click to toggle source

alias for journals

    # File lib/bio/io/ncbirest.rb
493 def journal(*args)
494   self.search("journals", *args)
495 end
method_missing(*args) click to toggle source

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

    # File lib/bio/io/ncbirest.rb
488 def method_missing(*args)
489   self.search(*args)
490 end
search(db, term, *args) click to toggle source

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”, {“reldate” => 365}, 5) # combination 2 search(“journals”, “bmc”, 10)

    # File lib/bio/io/ncbirest.rb
456 def search(db, term, *args)
457   limit = 100
458   hash = {}
459   args.each do |arg|
460     case arg
461     when Hash
462       hash.update(arg)
463     else
464       limit = arg.to_i
465     end
466   end
467   opts = { "db" => db }
468   opts.update(hash)
469   Bio::NCBI::REST.esearch(term, opts, limit)
470 end