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 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

est(*args)

alias for "nucest"

[Source]

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

gss(*args)

alias for "nucgss"

[Source]

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

journal(*args)

alias for journals

[Source]

         # File lib/bio/io/ncbirest.rb, line 354
    354:       def journal(*args)
    355:         self.search("journals", *args)
    356:       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 349
    349:       def method_missing(*args)
    350:         self.search(*args)
    351:       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 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]