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 436
436:       def count(db, term, hash = {})
437:         opts = { "db" => db }
438:         opts.update(hash)
439:         Bio::NCBI::REST.esearch_count(term, opts)
440:       end

alias for "nucest"

[Source]

     # File lib/bio/io/ncbirest.rb, line 459
459:       def est(*args)
460:         self.search("nucest", *args)
461:       end

alias for "nucgss"

[Source]

     # File lib/bio/io/ncbirest.rb, line 464
464:       def gss(*args)
465:         self.search("nucgss", *args)
466:       end

alias for journals

[Source]

     # 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)

[Source]

     # 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)

[Source]

     # 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

[Validate]