Module | Bio::NCBI::REST::ESearch::Methods |
In: |
lib/bio/io/ncbirest.rb
|
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:
Returns: | array of entry IDs or a number of results |
alias for "nucest"
# File lib/bio/io/ncbirest.rb, line 359 359: def est(*args) 360: self.search("nucest", *args) 361: end
alias for "nucgss"
# File lib/bio/io/ncbirest.rb, line 364 364: def gss(*args) 365: self.search("nucgss", *args) 366: end
alias for journals
# File lib/bio/io/ncbirest.rb, line 354 354: def journal(*args) 355: self.search("journals", *args) 356: 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 349 349: def method_missing(*args) 350: self.search(*args) 351: 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 317 317: def search(db, term, *args) 318: limit = 100 319: hash = {} 320: args.each do |arg| 321: case arg 322: when Hash 323: hash.update(arg) 324: else 325: limit = arg.to_i 326: end 327: end 328: opts = { "db" => db } 329: opts.update(hash) 330: Bio::NCBI::REST.esearch(term, opts, limit) 331: end