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, line 475
def count(db, term, hash = {})
  opts = { "db" => db }
  opts.update(hash)
  Bio::NCBI::REST.esearch_count(term, opts)
end
est(*args) click to toggle source

alias for “nucest”

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

alias for “nucgss”

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

alias for journals

# File lib/bio/io/ncbirest.rb, line 493
def journal(*args)
  self.search("journals", *args)
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, line 488
def method_missing(*args)
  self.search(*args)
end