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).

- eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchlit_help.html

## 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

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

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

- eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchlit_help.html

## 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

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

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

- eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchlit_help.html

## 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

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

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

- eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchlit_help.html

## 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

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

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

- eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html

     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

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

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

- eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchtax_help.html

## 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]