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 536 536: def journal(ids, format = "full", hash = {}) 537: case format 538: when "xml" 539: format = "full" 540: mode = "xml" 541: else 542: mode = "text" 543: end 544: opts = { "db" => "journals", "rettype" => format, "retmode" => mode } 545: opts.update(hash) 546: Bio::NCBI::REST.efetch(ids, opts) 547: 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 571 571: def omim(ids, format = "detailed", hash = {}) 572: case format 573: when "xml" 574: format = "full" 575: mode = "xml" 576: when "linkout" 577: format = "ExternalLink" 578: mode = "text" 579: else 580: mode = "text" 581: end 582: opts = { "db" => "omim", "rettype" => format, "retmode" => mode } 583: opts.update(hash) 584: Bio::NCBI::REST.efetch(ids, opts) 585: 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 502 502: def pmc(ids, format = "docsum", hash = {}) 503: case format 504: when "xml" 505: format = "medline" 506: mode = "xml" 507: else 508: mode = "text" 509: end 510: opts = { "db" => "pmc", "rettype" => format, "retmode" => mode } 511: Bio::NCBI::REST.efetch(ids, opts) 512: 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 466 466: def pubmed(ids, format = "medline", hash = {}) 467: case format 468: when "xml" 469: format = "medline" 470: mode = "xml" 471: else 472: mode = "text" 473: end 474: opts = { "db" => "pubmed", "rettype" => format, "retmode" => mode } 475: opts.update(hash) 476: Bio::NCBI::REST.efetch(ids, opts) 477: 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 427 427: def sequence(ids, format = "gb", hash = {}) 428: case format 429: when "xml" 430: format = "gbc" 431: end 432: opts = { "db" => "sequences", "rettype" => format } 433: opts.update(hash) 434: Bio::NCBI::REST.efetch(ids, opts) 435: 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 609 609: def taxonomy(ids, format = "docsum", hash = {}) 610: case format 611: when "xml" 612: format = "full" 613: mode = "xml" 614: else 615: mode = "text" 616: end 617: opts = { "db" => "taxonomy", "rettype" => format, "retmode" => mode } 618: Bio::NCBI::REST.efetch(ids, opts) 619: end