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(db, term, hash = {})

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

[Source]

     # File lib/bio/io/ncbirest.rb, line 329
329:       def count(db, term, hash = {})
330:         opts = { "db" => db }
331:         opts.update(hash)
332:         Bio::NCBI::REST.esearch_count(term, opts)
333:       end
est(*args)

alias for "nucest"

[Source]

     # File lib/bio/io/ncbirest.rb, line 352
352:       def est(*args)
353:         self.search("nucest", *args)
354:       end
gss(*args)

alias for "nucgss"

[Source]

     # File lib/bio/io/ncbirest.rb, line 357
357:       def gss(*args)
358:         self.search("nucgss", *args)
359:       end
journal(*args)

alias for journals

[Source]

     # File lib/bio/io/ncbirest.rb, line 347
347:       def journal(*args)
348:         self.search("journals", *args)
349:       end
method_missing(*args)

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 342
342:       def method_missing(*args)
343:         self.search(*args)
344:       end
search(db, term, *args)

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 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

[Validate]