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

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

www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch

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

eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi

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

Public Instance Methods

count (db, term, hash = {})

Source

    # 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

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

est (*args)

Source

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

alias for “nucest”

gss (*args)

Source

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

alias for “nucgss”

journal (*args)

Source

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

alias for journals

method_missing (*args)

Source

    # File lib/bio/io/ncbirest.rb
488 def method_missing(*args)
489   self.search(*args)
490 end

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

search (db, term, *args)

Source

    # 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

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)