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 459 459: def est(*args) 460: self.search("nucest", *args) 461: end
alias for "nucgss"
# File lib/bio/io/ncbirest.rb, line 464 464: def gss(*args) 465: self.search("nucgss", *args) 466: end
alias for journals
# File lib/bio/io/ncbirest.rb, line 454 454: def journal(*args) 455: self.search("journals", *args) 456: 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 449 449: def method_missing(*args) 450: self.search(*args) 451: 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 417 417: def search(db, term, *args) 418: limit = 100 419: hash = {} 420: args.each do |arg| 421: case arg 422: when Hash 423: hash.update(arg) 424: else 425: limit = arg.to_i 426: end 427: end 428: opts = { "db" => db } 429: opts.update(hash) 430: Bio::NCBI::REST.esearch(term, opts, limit) 431: end