Module | Bio::NCBI::REST::EFetch::Methods |
In: |
lib/bio/io/ncbirest.rb
|
Retrieve journal entries by given IDs using E-Utils (efetch).
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 543 543: def journal(ids, format = "full", hash = {}) 544: case format 545: when "xml" 546: format = "full" 547: mode = "xml" 548: else 549: mode = "text" 550: end 551: opts = { "db" => "journals", "rettype" => format, "retmode" => mode } 552: opts.update(hash) 553: Bio::NCBI::REST.efetch(ids, opts) 554: end
Retrieve OMIM entries by given IDs using E-Utils (efetch).
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 578 578: def omim(ids, format = "detailed", hash = {}) 579: case format 580: when "xml" 581: format = "full" 582: mode = "xml" 583: when "linkout" 584: format = "ExternalLink" 585: mode = "text" 586: else 587: mode = "text" 588: end 589: opts = { "db" => "omim", "rettype" => format, "retmode" => mode } 590: opts.update(hash) 591: Bio::NCBI::REST.efetch(ids, opts) 592: end
Retrieve PubMed Central entries by given IDs using E-Utils (efetch).
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 509 509: def pmc(ids, format = "docsum", hash = {}) 510: case format 511: when "xml" 512: format = "medline" 513: mode = "xml" 514: else 515: mode = "text" 516: end 517: opts = { "db" => "pmc", "rettype" => format, "retmode" => mode } 518: Bio::NCBI::REST.efetch(ids, opts) 519: end
Retrieve PubMed entries by given IDs using E-Utils (efetch).
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 473 473: def pubmed(ids, format = "medline", hash = {}) 474: case format 475: when "xml" 476: format = "medline" 477: mode = "xml" 478: else 479: mode = "text" 480: end 481: opts = { "db" => "pubmed", "rettype" => format, "retmode" => mode } 482: opts.update(hash) 483: Bio::NCBI::REST.efetch(ids, opts) 484: end
Retrieve sequence entries by given IDs using E-Utils (efetch).
sequences = gene + genome + nucleotide + protein + popset + snp nucleotide = nuccore + nucest + nucgss
format (rettype):
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 434 434: def sequence(ids, format = "gb", hash = {}) 435: case format 436: when "xml" 437: format = "gbc" 438: end 439: opts = { "db" => "sequences", "rettype" => format } 440: opts.update(hash) 441: Bio::NCBI::REST.efetch(ids, opts) 442: end
Retrieve taxonomy entries by given IDs using E-Utils (efetch).
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:
Returns: | String |
# File lib/bio/io/ncbirest.rb, line 616 616: def taxonomy(ids, format = "docsum", hash = {}) 617: case format 618: when "xml" 619: format = "full" 620: mode = "xml" 621: else 622: mode = "text" 623: end 624: opts = { "db" => "taxonomy", "rettype" => format, "retmode" => mode } 625: Bio::NCBI::REST.efetch(ids, opts) 626: end