# # = bio/io/ncbirest.rb - NCBI Entrez client module # # Copyright:: Copyright (C) 2008 Toshiaki Katayama # License:: The Ruby License # # $Id:$ # require 'thread' require 'bio/command' require 'bio/version' module Bio class NCBI # (Hash) Default parameters for Entrez (eUtils). # They may also be used for other NCBI services. ENTREZ_DEFAULT_PARAMETERS = { # Cited from # http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.Release_Notes # tool: # Name of application making the E-utility call. # Value must be a string with no internal spaces. 'tool' => "bioruby", # Cited from # http://www.ncbi.nlm.nih.gov/books/NBK25497/ # The value of email should be a complete and valid e-mail address # of the software developer and not that of a third-party end user. 'email' => 'staff@bioruby.org', } # Resets Entrez (eUtils) default parameters. # --- # *Returns*:: (Hash) default parameters def self.reset_entrez_default_parameters h = { 'tool' => "bioruby", 'email' => 'staff@bioruby.org', } ENTREZ_DEFAULT_PARAMETERS.clear ENTREZ_DEFAULT_PARAMETERS.update(h) end # Gets default email address for Entrez (eUtils). # --- # *Returns*:: String or nil def self.default_email ENTREZ_DEFAULT_PARAMETERS['email'] end # Sets default email address used for Entrez (eUtils). # It may also be used for other NCBI services. # # In http://www.ncbi.nlm.nih.gov/books/NBK25497/ # NCBI says: # "The value of email should be a complete and valid e-mail address of # the software developer and not that of a third-party end user." # # By default, email address of BioRuby staffs is set. # # From the above NCBI documentation, the tool and email value is used # only for unblocking IP addresses blocked by NCBI due to excess requests. # For the purpose, NCBI says: # "Please be aware that merely providing values for tool and email # in requests is not sufficient to comply with this policy; # these values must be registered with NCBI." # # Please use your own email address and tool name when registering # tool and email values to NCBI. # # --- # *Arguments*: # * (required) _str_: (String) email address # *Returns*:: same as given argument def self.default_email=(str) ENTREZ_DEFAULT_PARAMETERS['email'] = str end # Gets default tool name for Entrez (eUtils). # --- # *Returns*:: String or nil def self.default_tool ENTREZ_DEFAULT_PARAMETERS['tool'] end # Sets default tool name for Entrez (eUtils). # It may also be used for other NCBI services. # # In http://www.ncbi.nlm.nih.gov/books/NBK25497/ # NCBI says: # "The value of tool should be a string with no internal spaces that # uniquely identifies the software producing the request." # # "bioruby" is set by default. # Please use your own tool name when registering to NCBI. # # See the document of default_email= for more information. # # --- # *Arguments*: # * (required) _str_: (String) tool name # *Returns*:: same as given argument def self.default_tool=(str) ENTREZ_DEFAULT_PARAMETERS['tool'] = str end # == Description # # The Bio::NCBI::REST class provides REST client for the NCBI E-Utilities # # Entrez utilities index: # # * http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html # class REST # 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.". NCBI_INTERVAL = 1.0 / 3.0 @@last_access = nil @@last_access_mutex = nil private # (Private) Sleeps until allowed to access. # --- # *Arguments*: # * (required) _wait_: wait unit time # *Returns*:: (undefined) def ncbi_access_wait(wait = NCBI_INTERVAL) @@last_access_mutex ||= Mutex.new @@last_access_mutex.synchronize { if @@last_access duration = Time.now - @@last_access if wait > duration sleep wait - duration end end @@last_access = Time.now } nil end # (Private) default parameters # --- # *Returns*:: Hash def default_parameters Bio::NCBI::ENTREZ_DEFAULT_PARAMETERS end # (Private) Sends query to NCBI. # --- # *Arguments*: # * (required) _serv_: (String) server URI string # * (required) _opts_: (Hash) parameters # *Returns*:: nil def ncbi_post_form(serv, opts) ncbi_check_parameters(opts) ncbi_access_wait #$stderr.puts opts.inspect response = Bio::Command.post_form(serv, opts) response end # (Private) Checks parameters as NCBI requires. # If no email or tool parameter, raises an error. # # NCBI announces that "Effective on # June 1, 2010, all E-utility requests, either using standard URLs or # SOAP, must contain non-null values for both the &tool and &email # parameters. Any E-utility request made after June 1, 2010 that does # not contain values for both parameters will return an error explaining # that these parameters must be included in E-utility requests." # --- # *Arguments*: # * (required) _opts_: Hash containing parameters # *Returns*:: (undefined) def ncbi_check_parameters(opts) #return if Time.now < Time.gm(2010,5,31) if opts['email'].to_s.empty? then raise 'Set email parameter for the query, or set Bio::NCBI.default_email = "(email address of the author of this software)"' end if opts['tool'].to_s.empty? then raise 'Set tool parameter for the query, or set Bio::NCBI.default_tool = "(your tool name)"' end nil end public # List the NCBI database names E-Utils (einfo) service # # * http://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 # # ncbi = Bio::NCBI::REST.new # ncbi.einfo # # Bio::NCBI::REST.einfo # # --- # *Returns*:: array of string (database names) 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>/m).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 # # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html # * http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Search_Field_Descrip # # == Usage # # 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 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>/m).flatten end return list end end # *Arguments*:: same as esearch method # *Returns*:: array of entry IDs or a number of results 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>/m).flatten.first.to_i return count end # Retrieve database entries by given IDs and using E-Utils (efetch) service. # # For information on the possible arguments, see # # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html # # == Usage # # 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*:: String 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 def self.einfo self.new.einfo end def self.esearch(*args) self.new.esearch(*args) end def self.esearch_count(*args) self.new.esearch_count(*args) end def self.efetch(*args) self.new.efetch(*args) end # Shortcut methods for the ESearch service class ESearch # Search database entries by given keywords using E-Utils (esearch). # # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html # # sequences = gene + genome + nucleotide + protein + popset + snp # nucleotide = nuccore + nucest + nucgss # # * http://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 module Methods # 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) def search(db, term, *args) limit = 100 hash = {} args.each do |arg| case arg when Hash hash.update(arg) else limit = arg.to_i end end opts = { "db" => db } opts.update(hash) Bio::NCBI::REST.esearch(term, opts, limit) end # count("nucleotide", "tardigrada") # count("pubmed", "tardigrada") # count("journals", "bmc") def count(db, term, hash = {}) opts = { "db" => db } opts.update(hash) Bio::NCBI::REST.esearch_count(term, opts) 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) def method_missing(*args) self.search(*args) end # alias for journals def journal(*args) self.search("journals", *args) end # alias for "nucest" def est(*args) self.search("nucest", *args) end # alias for "nucgss" def gss(*args) self.search("nucgss", *args) end end # Methods include Methods extend Methods end # ESearch # Shortcut methods for the EFetch service class EFetch module Methods # Retrieve sequence entries by given IDs using E-Utils (efetch). # # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html # # sequences = gene + genome + nucleotide + protein + popset + snp # nucleotide = nuccore + nucest + nucgss # # format (rettype): # * native all but Gene ASN Default format for viewing sequences # * fasta all sequence FASTA view of a sequence # * gb NA sequence GenBank view for sequences # * gbc NA sequence INSDSeq structured flat file # * gbwithparts NA sequence GenBank CON division with sequences # * est dbEST sequence EST Report # * gss dbGSS sequence GSS Report # * gp AA sequence GenPept view # * gpc AA sequence INSDSeq structured flat file # * seqid all sequence Convert GIs into seqids # * acc all sequence Convert GIs into accessions # * chr dbSNP only SNP Chromosome Report # * flt dbSNP only SNP Flat File report # * rsr dbSNP only SNP RS Cluster report # * brief dbSNP only SNP ID list # * docset dbSNP only SNP RS summary # # == Usage # # Bio::NCBI::REST::EFetch.sequence("123,U12345,U12345.1,gb|U12345|") # # list = [123, "U12345.1", "gb|U12345|"] # Bio::NCBI::REST::EFetch.sequence(list) # Bio::NCBI::REST::EFetch.sequence(list, "fasta") # Bio::NCBI::REST::EFetch.sequence(list, "acc") # Bio::NCBI::REST::EFetch.sequence(list, "xml") # # Bio::NCBI::REST::EFetch.sequence("AE009950") # Bio::NCBI::REST::EFetch.sequence("AE009950", "gbwithparts") # # ncbi = Bio::NCBI::REST::EFetch.new # ncbi.sequence("123,U12345,U12345.1,gb|U12345|") # ncbi.sequence(list) # ncbi.sequence(list, "fasta") # ncbi.sequence(list, "acc") # ncbi.sequence(list, "xml") # ncbi.sequence("AE009950") # ncbi.sequence("AE009950", "gbwithparts") # # --- # # *Arguments*: # * _ids_: list of NCBI entry IDs (required) # * _format_: "gb", "gbc", "fasta", "acc", "xml" etc. # *Returns*:: String def sequence(ids, format = "gb", hash = {}) case format when "xml" format = "gbc" end opts = { "db" => "sequences", "rettype" => format } opts.update(hash) Bio::NCBI::REST.efetch(ids, opts) end # Retrieve nucleotide sequence entries by given IDs using E-Utils # (efetch). # # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html # nucleotide = nuccore + nucest + nucgss # # format (rettype): # * native all but Gene ASN Default format for viewing sequences # * fasta all sequence FASTA view of a sequence # * gb NA sequence GenBank view for sequences # * gbc NA sequence INSDSeq structured flat file # * gbwithparts NA sequence GenBank CON division with sequences # * est dbEST sequence EST Report # * gss dbGSS sequence GSS Report # * gp AA sequence GenPept view # * gpc AA sequence INSDSeq structured flat file # * seqid all sequence Convert GIs into seqids # * acc all sequence Convert GIs into accessions # * chr dbSNP only SNP Chromosome Report # * flt dbSNP only SNP Flat File report # * rsr dbSNP only SNP RS Cluster report # * brief dbSNP only SNP ID list # * docset dbSNP only SNP RS summary # # == Usage # # Bio::NCBI::REST::EFetch.nucleotide("123,U12345,U12345.1,gb|U12345|") # # list = [123, "U12345.1", "gb|U12345|"] # Bio::NCBI::REST::EFetch.nucleotide(list) # Bio::NCBI::REST::EFetch.nucleotide(list, "fasta") # Bio::NCBI::REST::EFetch.nucleotide(list, "acc") # Bio::NCBI::REST::EFetch.nucleotide(list, "xml") # # Bio::NCBI::REST::EFetch.nucleotide("AE009950") # Bio::NCBI::REST::EFetch.nucleotide("AE009950", "gbwithparts") # # ncbi = Bio::NCBI::REST::EFetch.new # ncbi.nucleotide("123,U12345,U12345.1,gb|U12345|") # ncbi.nucleotide(list) # ncbi.nucleotide(list, "fasta") # ncbi.nucleotide(list, "acc") # ncbi.nucleotide(list, "xml") # ncbi.nucleotide("AE009950") # ncbi.nucleotide("AE009950", "gbwithparts") # # --- # # *Arguments*: # * _ids_: list of NCBI entry IDs (required) # * _format_: "gb", "gbc", "fasta", "acc", "xml" etc. # *Returns*:: String def nucleotide(ids, format = "gb", hash = {}) case format when "xml" format = "gbc" end opts = { "db" => "nucleotide", "rettype" => format } opts.update(hash) Bio::NCBI::REST.efetch(ids, opts) end # Retrieve protein sequence entries by given IDs using E-Utils # (efetch). # # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html # protein # # format (rettype): # * native all but Gene ASN Default format for viewing sequences # * fasta all sequence FASTA view of a sequence # * gb NA sequence GenBank view for sequences # * gbc NA sequence INSDSeq structured flat file # * gbwithparts NA sequence GenBank CON division with sequences # * est dbEST sequence EST Report # * gss dbGSS sequence GSS Report # * gp AA sequence GenPept view # * gpc AA sequence INSDSeq structured flat file # * seqid all sequence Convert GIs into seqids # * acc all sequence Convert GIs into accessions # * chr dbSNP only SNP Chromosome Report # * flt dbSNP only SNP Flat File report # * rsr dbSNP only SNP RS Cluster report # * brief dbSNP only SNP ID list # * docset dbSNP only SNP RS summary # # == Usage # # Bio::NCBI::REST::EFetch.protein("7527480,AAF63163.1,AAF63163") # # list = [ 7527480, "AAF63163.1", "AAF63163"] # Bio::NCBI::REST::EFetch.protein(list) # Bio::NCBI::REST::EFetch.protein(list, "fasta") # Bio::NCBI::REST::EFetch.protein(list, "acc") # Bio::NCBI::REST::EFetch.protein(list, "xml") # # ncbi = Bio::NCBI::REST::EFetch.new # ncbi.protein("7527480,AAF63163.1,AAF63163") # ncbi.protein(list) # ncbi.protein(list, "fasta") # ncbi.protein(list, "acc") # ncbi.protein(list, "xml") # # --- # # *Arguments*: # * _ids_: list of NCBI entry IDs (required) # * _format_: "gp", "gpc", "fasta", "acc", "xml" etc. # *Returns*:: String def protein(ids, format = "gp", hash = {}) case format when "xml" format = "gpc" end opts = { "db" => "protein", "rettype" => format } opts.update(hash) Bio::NCBI::REST.efetch(ids, opts) end # Retrieve PubMed entries by given IDs using E-Utils (efetch). # # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchlit_help.html # # == Usage # # Bio::NCBI::REST::EFetch.pubmed(15496913) # Bio::NCBI::REST::EFetch.pubmed("15496913,11181995") # # list = [15496913, 11181995] # Bio::NCBI::REST::EFetch.pubmed(list) # Bio::NCBI::REST::EFetch.pubmed(list, "abstract") # Bio::NCBI::REST::EFetch.pubmed(list, "citation") # Bio::NCBI::REST::EFetch.pubmed(list, "medline") # Bio::NCBI::REST::EFetch.pubmed(list, "xml") # # ncbi = Bio::NCBI::REST::EFetch.new # ncbi.pubmed(list) # ncbi.pubmed(list, "abstract") # ncbi.pubmed(list, "citation") # ncbi.pubmed(list, "medline") # ncbi.pubmed(list, "xml") # # --- # # *Arguments*: # * _ids_: list of PubMed entry IDs (required) # * _format_: "abstract", "citation", "medline", "xml" # *Returns*:: String def pubmed(ids, format = "medline", hash = {}) case format when "xml" format = "medline" mode = "xml" else mode = "text" end opts = { "db" => "pubmed", "rettype" => format, "retmode" => mode } opts.update(hash) Bio::NCBI::REST.efetch(ids, opts) end # Retrieve PubMed Central entries by given IDs using E-Utils (efetch). # # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchlit_help.html # # == Usage # # Bio::NCBI::REST::EFetch.pmc(1360101) # Bio::NCBI::REST::EFetch.pmc("1360101,534663") # # list = [1360101, 534663] # Bio::NCBI::REST::EFetch.pmc(list) # Bio::NCBI::REST::EFetch.pmc(list, "xml") # # ncbi = Bio::NCBI::REST::EFetch.new # ncbi.pmc(list) # ncbi.pmc(list, "xml") # # --- # # *Arguments*: # * _ids_: list of PubMed Central entry IDs (required) # * _format_: "docsum", "xml" # *Returns*:: String def pmc(ids, format = "docsum", hash = {}) case format when "xml" format = "medline" mode = "xml" else mode = "text" end opts = { "db" => "pmc", "rettype" => format, "retmode" => mode } Bio::NCBI::REST.efetch(ids, opts) end # Retrieve journal entries by given IDs using E-Utils (efetch). # # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchlit_help.html # # == Usage # # Bio::NCBI::REST::EFetch.journal(21854) # # list = [21854, 21855] # Bio::NCBI::REST::EFetch.journal(list) # Bio::NCBI::REST::EFetch.journal(list, "xml") # # ncbi = Bio::NCBI::REST::EFetch.new # ncbi.journal(list) # ncbi.journal(list, "xml") # # --- # # *Arguments*: # * _ids_: list of journal entry IDs (required) # * _format_: "full", "xml" # *Returns*:: String def journal(ids, format = "full", hash = {}) case format when "xml" format = "full" mode = "xml" else mode = "text" end opts = { "db" => "journals", "rettype" => format, "retmode" => mode } opts.update(hash) Bio::NCBI::REST.efetch(ids, opts) end # Retrieve OMIM entries by given IDs using E-Utils (efetch). # # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchlit_help.html # # == Usage # # Bio::NCBI::REST::EFetch.omim(143100) # # list = [143100, 602260] # Bio::NCBI::REST::EFetch.omim(list) # Bio::NCBI::REST::EFetch.omim(list, "xml") # # ncbi = Bio::NCBI::REST::EFetch.new # ncbi.omim(list) # ncbi.omim(list, "xml") # # --- # # *Arguments*: # * _ids_: list of OMIM entry IDs (required) # * _format_: "docsum", "synopsis", "variants", "detailed", "linkout", "xml" # *Returns*:: String def omim(ids, format = "detailed", hash = {}) case format when "xml" format = "full" mode = "xml" when "linkout" format = "ExternalLink" mode = "text" else mode = "text" end opts = { "db" => "omim", "rettype" => format, "retmode" => mode } opts.update(hash) Bio::NCBI::REST.efetch(ids, opts) end # Retrieve taxonomy entries by given IDs using E-Utils (efetch). # # * http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchtax_help.html # # == Usage # # Bio::NCBI::REST::EFetch.taxonomy(42241) # # list = [232323, 290179, 286681] # Bio::NCBI::REST::EFetch.taxonomy(list) # Bio::NCBI::REST::EFetch.taxonomy(list, "xml") # # ncbi = Bio::NCBI::REST::EFetch.new # ncbi.taxonomy(list) # ncbi.taxonomy(list, "xml") # # --- # # *Arguments*: # * _ids_: list of Taxonomy entry IDs (required) # * _format_: "brief", "docsum", "xml" # *Returns*:: String def taxonomy(ids, format = "docsum", hash = {}) case format when "xml" format = "full" mode = "xml" else mode = "text" end opts = { "db" => "taxonomy", "rettype" => format, "retmode" => mode } Bio::NCBI::REST.efetch(ids, opts) end end # Methods include Methods extend Methods end # EFetch end # REST end # NCBI end # Bio