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 543
543:       def journal(ids, format = "full", hash = {})
544:         case format
545:         when "xml"
546:           format = "full"
547:           mode = "xml"
548:         else
549:           mode = "text"
550:         end
551:         opts = { "db" => "journals", "rettype" => format, "retmode" => mode }
552:         opts.update(hash)
553:         Bio::NCBI::REST.efetch(ids, opts)
554:       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 578
578:       def omim(ids, format = "detailed", hash = {})
579:         case format
580:         when "xml"
581:           format = "full"
582:           mode = "xml"
583:         when "linkout"
584:           format = "ExternalLink"
585:           mode = "text"
586:         else
587:           mode = "text"
588:         end
589:         opts = { "db" => "omim", "rettype" => format, "retmode" => mode }
590:         opts.update(hash)
591:         Bio::NCBI::REST.efetch(ids, opts)
592:       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 509
509:       def pmc(ids, format = "docsum", hash = {})
510:         case format
511:         when "xml"
512:           format = "medline"
513:           mode = "xml"
514:         else
515:           mode = "text"
516:         end
517:         opts = { "db" => "pmc", "rettype" => format, "retmode" => mode }
518:         Bio::NCBI::REST.efetch(ids, opts)
519:       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 473
473:       def pubmed(ids, format = "medline", hash = {})
474:         case format
475:         when "xml"
476:           format = "medline"
477:           mode = "xml"
478:         else
479:           mode = "text"
480:         end
481:         opts = { "db" => "pubmed", "rettype" => format, "retmode" => mode }
482:         opts.update(hash)
483:         Bio::NCBI::REST.efetch(ids, opts)
484:       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 434
434:       def sequence(ids, format = "gb", hash = {})
435:         case format
436:         when "xml"
437:           format = "gbc"
438:         end
439:         opts = { "db" => "sequences", "rettype" => format }
440:         opts.update(hash)
441:         Bio::NCBI::REST.efetch(ids, opts)
442:       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 616
616:       def taxonomy(ids, format = "docsum", hash = {})
617:         case format
618:         when "xml"
619:           format = "full"
620:           mode = "xml"
621:         else
622:           mode = "text"
623:         end
624:         opts = { "db" => "taxonomy", "rettype" => format, "retmode" => mode }
625:         Bio::NCBI::REST.efetch(ids, opts)
626:       end

[Validate]