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

Usage

 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

Methods

count   est   gss   journal   method_missing   search  

Public Instance methods

count("nucleotide", "tardigrada") count("pubmed", "tardigrada") count("journals", "bmc")

[Source]

     # File lib/bio/io/ncbirest.rb, line 336
336:       def count(db, term, hash = {})
337:         opts = { "db" => db }
338:         opts.update(hash)
339:         Bio::NCBI::REST.esearch_count(term, opts)
340:       end

alias for "nucest"

[Source]

     # File lib/bio/io/ncbirest.rb, line 359
359:       def est(*args)
360:         self.search("nucest", *args)
361:       end

alias for "nucgss"

[Source]

     # File lib/bio/io/ncbirest.rb, line 364
364:       def gss(*args)
365:         self.search("nucgss", *args)
366:       end

alias for journals

[Source]

     # 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)

[Source]

     # 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)

[Source]

     # 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

[Validate]