The Bio::NCBI::REST class provides REST client for the NCBI E-Utilities
Entrez utilities index:
Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests. -> Not implemented yet in BioRuby
Wait for 1/3 seconds. NCBI’s restriction is: “Make no more than 3 requests every 1 second.”.
# File lib/bio/io/ncbirest.rb, line 352 def self.efetch(*args) self.new.efetch(*args) end
# File lib/bio/io/ncbirest.rb, line 340 def self.einfo self.new.einfo end
Retrieve database entries by given IDs and using E-Utils (efetch) service.
For information on the possible arguments, see
ncbi = Bio::NCBI::REST.new ncbi.efetch("185041", {"db"=>"nucleotide", "rettype"=>"gb", "retmode" => "xml"}) ncbi.efetch("J00231", {"db"=>"nuccore", "rettype"=>"gb", "retmode"=>"xml"}) ncbi.efetch("AAA52805", {"db"=>"protein", "rettype"=>"gb"}) Bio::NCBI::REST.efetch("185041", {"db"=>"nucleotide", "rettype"=>"gb", "retmode" => "xml"}) Bio::NCBI::REST.efetch("J00231", {"db"=>"nuccore", "rettype"=>"gb"}) Bio::NCBI::REST.efetch("AAA52805", {"db"=>"protein", "rettype"=>"gb"})
Arguments:
ids: list of NCBI entry IDs (required)
hash: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
db: "sequences", "nucleotide", "protein", "pubmed", "omim", ...
retmode: "text", "xml", "html", ...
rettype: "gb", "gbc", "medline", "count",...
step: maximum number of entries retrieved at a time
Returns |
# File lib/bio/io/ncbirest.rb, line 316 def efetch(ids, hash = {}, step = 100) serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi" opts = default_parameters.merge({ "retmode" => "text" }) opts.update(hash) case ids when Array list = ids else list = ids.to_s.split(/\s*,\s*/) end result = "" 0.step(list.size, step) do |i| opts["id"] = list[i, step].join(',') unless opts["id"].empty? response = ncbi_post_form(serv, opts) result += response.body end end return result.strip #return result.strip.split(/\n\n+/) end
List the NCBI database names E-Utils (einfo) service
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
ncbi = Bio::NCBI::REST.new ncbi.einfo Bio::NCBI::REST.einfo
Returns |
array of string (database names) |
# File lib/bio/io/ncbirest.rb, line 180 def einfo serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi" opts = default_parameters.merge({}) response = ncbi_post_form(serv, opts) result = response.body list = result.scan(/<DbName>(.*?)<\/DbName>/).flatten return list end
Search the NCBI database by given keywords using E-Utils (esearch) service and returns an array of entry IDs.
For information on the possible arguments, see
eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Search_Field_Descrip
ncbi = Bio::NCBI::REST.new ncbi.esearch("tardigrada", {"db"=>"nucleotide", "rettype"=>"count"}) ncbi.esearch("tardigrada", {"db"=>"nucleotide", "rettype"=>"gb"}) ncbi.esearch("yeast kinase", {"db"=>"nuccore", "rettype"=>"gb", "retmax"=>5}) Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nucleotide", "rettype"=>"count"}) Bio::NCBI::REST.esearch("tardigrada", {"db"=>"nucleotide", "rettype"=>"gb"}) Bio::NCBI::REST.esearch("yeast kinase", {"db"=>"nuccore", "rettype"=>"gb", "retmax"=>5})
Arguments:
str: query string (required)
hash: hash of E-Utils option {"db" => "nuccore", "rettype" => "gb"}
db: "sequences", "nucleotide", "protein", "pubmed", "taxonomy", ...
retmode: "text", "xml", "html", ...
rettype: "gb", "medline", "count", ...
retmax: integer (default 100)
retstart: integer
field:
“titl”: Title [TI]
“tiab”: Title/Abstract [TIAB]
“word”: Text words [TW]
“auth”: Author [AU]
“affl”: Affiliation [AD]
“jour”: Journal [TA]
“vol”: Volume [VI]
“iss”: Issue [IP]
“page”: First page [PG]
“pdat”: Publication date [DP]
“ptyp”: Publication type [PT]
“lang”: Language [LA]
“mesh”: MeSH term [MH]
“majr”: MeSH major topic [MAJR]
“subh”: Mesh sub headings [SH]
“mhda”: MeSH date [MHDA]
“ecno”: EC/RN Number [rn]
“si”: Secondary source ID [SI]
“uid”: PubMed ID (PMID) [UI]
“fltr”: Filter [FILTER] [SB]
“subs”: Subset [SB]
reldate: 365
mindate: 2001
maxdate: 2002/01/01
datetype: "edat"
limit: maximum number of entries to be returned (0 for unlimited; nil for the "retmax" value in the hash or the internal default value (=100))
step: maximum number of entries retrieved at a time
Returns |
array of entry IDs or a number of results |
# File lib/bio/io/ncbirest.rb, line 247 def esearch(str, hash = {}, limit = nil, step = 10000) serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" opts = default_parameters.merge({ "term" => str }) opts.update(hash) case opts["rettype"] when "count" count = esearch_count(str, opts) return count else retstart = 0 retstart = hash["retstart"].to_i if hash["retstart"] limit ||= hash["retmax"].to_i if hash["retmax"] limit ||= 100 # default limit is 100 limit = esearch_count(str, opts) if limit == 0 # unlimit list = [] 0.step(limit, step) do |i| retmax = [step, limit - i].min opts.update("retmax" => retmax, "retstart" => i + retstart) response = ncbi_post_form(serv, opts) result = response.body list += result.scan(/<Id>(.*?)<\/Id>/).flatten end return list end end
Arguments |
same as esearch method |
Returns |
array of entry IDs or a number of results |
# File lib/bio/io/ncbirest.rb, line 278 def esearch_count(str, hash = {}) serv = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" opts = default_parameters.merge({ "term" => str }) opts.update(hash) opts.update("rettype" => "count") response = ncbi_post_form(serv, opts) result = response.body count = result.scan(/<Count>(.*?)<\/Count>/).flatten.first.to_i return count end
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