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

Methods

journal   omim   pmc   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 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).

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 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).

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 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).

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 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):

  • native all but Gene 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 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).

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 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

[Validate]