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 642 642: def journal(ids, format = "full", hash = {}) 643: case format 644: when "xml" 645: format = "full" 646: mode = "xml" 647: else 648: mode = "text" 649: end 650: opts = { "db" => "journals", "rettype" => format, "retmode" => mode } 651: opts.update(hash) 652: Bio::NCBI::REST.efetch(ids, opts) 653: 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 677 677: def omim(ids, format = "detailed", hash = {}) 678: case format 679: when "xml" 680: format = "full" 681: mode = "xml" 682: when "linkout" 683: format = "ExternalLink" 684: mode = "text" 685: else 686: mode = "text" 687: end 688: opts = { "db" => "omim", "rettype" => format, "retmode" => mode } 689: opts.update(hash) 690: Bio::NCBI::REST.efetch(ids, opts) 691: 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 608 608: def pmc(ids, format = "docsum", hash = {}) 609: case format 610: when "xml" 611: format = "medline" 612: mode = "xml" 613: else 614: mode = "text" 615: end 616: opts = { "db" => "pmc", "rettype" => format, "retmode" => mode } 617: Bio::NCBI::REST.efetch(ids, opts) 618: 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 572 572: def pubmed(ids, format = "medline", hash = {}) 573: case format 574: when "xml" 575: format = "medline" 576: mode = "xml" 577: else 578: mode = "text" 579: end 580: opts = { "db" => "pubmed", "rettype" => format, "retmode" => mode } 581: opts.update(hash) 582: Bio::NCBI::REST.efetch(ids, opts) 583: 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 533 533: def sequence(ids, format = "gb", hash = {}) 534: case format 535: when "xml" 536: format = "gbc" 537: end 538: opts = { "db" => "sequences", "rettype" => format } 539: opts.update(hash) 540: Bio::NCBI::REST.efetch(ids, opts) 541: 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 715 715: def taxonomy(ids, format = "docsum", hash = {}) 716: case format 717: when "xml" 718: format = "full" 719: mode = "xml" 720: else 721: mode = "text" 722: end 723: opts = { "db" => "taxonomy", "rettype" => format, "retmode" => mode } 724: Bio::NCBI::REST.efetch(ids, opts) 725: end