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 458 458: def est(*args) 459: self.search("nucest", *args) 460: end
alias for "nucgss"
# File lib/bio/io/ncbirest.rb, line 463 463: def gss(*args) 464: self.search("nucgss", *args) 465: end
alias for journals
# File lib/bio/io/ncbirest.rb, line 453 453: def journal(*args) 454: self.search("journals", *args) 455: 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 448 448: def method_missing(*args) 449: self.search(*args) 450: 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 416 416: def search(db, term, *args) 417: limit = 100 418: hash = {} 419: args.each do |arg| 420: case arg 421: when Hash 422: hash.update(arg) 423: else 424: limit = arg.to_i 425: end 426: end 427: opts = { "db" => db } 428: opts.update(hash) 429: Bio::NCBI::REST.esearch(term, opts, limit) 430: end