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
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 |
count("nucleotide", "tardigrada") count("pubmed", "tardigrada") count("journals", "bmc")
# 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
alias for "nucest"
# File lib/bio/io/ncbirest.rb, line 459 def est(*args) self.search("nucest", *args) end
alias for "nucgss"
# File lib/bio/io/ncbirest.rb, line 464 def gss(*args) self.search("nucgss", *args) end
alias for journals
# File lib/bio/io/ncbirest.rb, line 454 def journal(*args) self.search("journals", *args) 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)
# File lib/bio/io/ncbirest.rb, line 449 def method_missing(*args) self.search(*args) 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)
# 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
Generated with the Darkfish Rdoc Generator 2.