Module | Bio::NCBI::REST::ESearch::Methods
In: | lib/bio/io/ncbirest.rb

Search database entries by given keywords using E-Utils (esearch).

- eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html

     sequences = gene + genome + nucleotide + protein + popset + snp
     nucleotide = nuccore + nucest + nucgss

- eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi

     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 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

est(*args)

alias for "nucest"

[Source]

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

gss(*args)

alias for "nucgss"

[Source]

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

journal(*args)

alias for journals

[Source]

         # File lib/bio/io/ncbirest.rb, line 454
    454:       def journal(*args)
    455:         self.search("journals", *args)
    456:       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 449
    449:       def method_missing(*args)
    450:         self.search(*args)
    451:       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 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]