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

Methods

journal   omim   pmc   pubmed   sequence   taxonomy  

Public Instance methods

journal(ids, format = "full", hash = {})

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 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
omim(ids, format = "detailed", hash = {})

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 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
pmc(ids, format = "docsum", hash = {})

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 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
pubmed(ids, format = "medline", hash = {})

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 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
sequence(ids, format = "gb", hash = {})

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 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
taxonomy(ids, format = "docsum", hash = {})

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 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

[Validate]