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 352 352: def est(*args) 353: self.search("nucest", *args) 354: end
alias for "nucgss"
# File lib/bio/io/ncbirest.rb, line 357 357: def gss(*args) 358: self.search("nucgss", *args) 359: end
alias for journals
# File lib/bio/io/ncbirest.rb, line 347 347: def journal(*args) 348: self.search("journals", *args) 349: 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 342 342: def method_missing(*args) 343: self.search(*args) 344: 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 310 310: def search(db, term, *args) 311: limit = 100 312: hash = {} 313: args.each do |arg| 314: case arg 315: when Hash 316: hash.update(arg) 317: else 318: limit = arg.to_i 319: end 320: end 321: opts = { "db" => db } 322: opts.update(hash) 323: Bio::NCBI::REST.esearch(term, opts, limit) 324: end