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:
ids: list of journal entry IDs (required)
format: "full", "xml"
Returns |
# File lib/bio/io/ncbirest.rb, line 762 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 nucleotide sequence entries by given IDs using E-Utils (efetch).
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
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 |
# File lib/bio/io/ncbirest.rb, line 596 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 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:
ids: list of OMIM entry IDs (required)
format: "docsum", "synopsis", "variants", "detailed", "linkout", "xml"
Returns |
# File lib/bio/io/ncbirest.rb, line 797 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 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:
ids: list of PubMed Central entry IDs (required)
format: "docsum", "xml"
Returns |
# File lib/bio/io/ncbirest.rb, line 728 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 protein sequence entries by given IDs using E-Utils (efetch).
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
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 |
# File lib/bio/io/ncbirest.rb, line 653 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).
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 |
# File lib/bio/io/ncbirest.rb, line 692 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 sequence entries by given IDs using E-Utils (efetch).
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
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 |
# File lib/bio/io/ncbirest.rb, line 534 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 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:
ids: list of Taxonomy entry IDs (required)
format: "brief", "docsum", "xml"
Returns |
# File lib/bio/io/ncbirest.rb, line 835 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
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