Module Bio::NCBI::REST::EFetch::Methods
In: lib/bio/io/ncbirest.rb

Methods

journal   nucleotide   omim   pmc   protein   pubmed   sequence   taxonomy  

Public Instance methods

Retrieve journal entries by given IDs using E-Utils (efetch).

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

[Source]

     # File lib/bio/io/ncbirest.rb, line 762
762:       def journal(ids, format = "full", hash = {})
763:         case format
764:         when "xml"
765:           format = "full"
766:           mode = "xml"
767:         else
768:           mode = "text"
769:         end
770:         opts = { "db" => "journals", "rettype" => format, "retmode" => mode }
771:         opts.update(hash)
772:         Bio::NCBI::REST.efetch(ids, opts)
773:       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

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

[Source]

     # File lib/bio/io/ncbirest.rb, line 596
596:       def nucleotide(ids, format = "gb", hash = {})
597:         case format
598:         when "xml"
599:           format = "gbc"
600:         end
601:         opts = { "db" => "nucleotide", "rettype" => format }
602:         opts.update(hash)
603:         Bio::NCBI::REST.efetch(ids, opts)
604:       end

Retrieve OMIM entries by given IDs using E-Utils (efetch).

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

[Source]

     # File lib/bio/io/ncbirest.rb, line 797
797:       def omim(ids, format = "detailed", hash = {})
798:         case format
799:         when "xml"
800:           format = "full"
801:           mode = "xml"
802:         when "linkout"
803:           format = "ExternalLink"
804:           mode = "text"
805:         else
806:           mode = "text"
807:         end
808:         opts = { "db" => "omim", "rettype" => format, "retmode" => mode }
809:         opts.update(hash)
810:         Bio::NCBI::REST.efetch(ids, opts)
811:       end

Retrieve PubMed Central entries by given IDs using E-Utils (efetch).

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

[Source]

     # File lib/bio/io/ncbirest.rb, line 728
728:       def pmc(ids, format = "docsum", hash = {})
729:         case format
730:         when "xml"
731:           format = "medline"
732:           mode = "xml"
733:         else
734:           mode = "text"
735:         end
736:         opts = { "db" => "pmc", "rettype" => format, "retmode" => mode }
737:         Bio::NCBI::REST.efetch(ids, opts)
738:       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

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

[Source]

     # File lib/bio/io/ncbirest.rb, line 653
653:       def protein(ids, format = "gp", hash = {})
654:         case format
655:         when "xml"
656:           format = "gpc"
657:         end
658:         opts = { "db" => "protein", "rettype" => format }
659:         opts.update(hash)
660:         Bio::NCBI::REST.efetch(ids, opts)
661:       end

Retrieve PubMed entries by given IDs using E-Utils (efetch).

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

[Source]

     # File lib/bio/io/ncbirest.rb, line 692
692:       def pubmed(ids, format = "medline", hash = {})
693:         case format
694:         when "xml"
695:           format = "medline"
696:           mode = "xml"
697:         else
698:           mode = "text"
699:         end
700:         opts = { "db" => "pubmed", "rettype" => format, "retmode" => mode }
701:         opts.update(hash)
702:         Bio::NCBI::REST.efetch(ids, opts)
703:       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

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

[Source]

     # File lib/bio/io/ncbirest.rb, line 534
534:       def sequence(ids, format = "gb", hash = {})
535:         case format
536:         when "xml"
537:           format = "gbc"
538:         end
539:         opts = { "db" => "sequences", "rettype" => format }
540:         opts.update(hash)
541:         Bio::NCBI::REST.efetch(ids, opts)
542:       end

Retrieve taxonomy entries by given IDs using E-Utils (efetch).

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

[Source]

     # File lib/bio/io/ncbirest.rb, line 835
835:       def taxonomy(ids, format = "docsum", hash = {})
836:         case format
837:         when "xml"
838:           format = "full"
839:           mode = "xml"
840:         else
841:           mode = "text"
842:         end
843:         opts = { "db" => "taxonomy", "rettype" => format, "retmode" => mode }
844:         Bio::NCBI::REST.efetch(ids, opts)
845:       end

[Validate]