spider (version 1.2-0)

read.BOLD: Downloads DNA sequences from the Barcode of Life Database (BOLD)

Description

These functions allow DNA sequences to be downloaded from the Barcode of Life Database (BOLD).

Usage

search.BOLD(taxon, exhaustive = FALSE)
stats.BOLD(taxon)
read.BOLD(IDs)

Arguments

taxon

A character vector of the names of the taxa of interest.

exhaustive

Logical. Should the function search for more than 500 process IDs? Default of FALSE.

IDs

A character vector containing BOLD process ID numbers.

Value

• search.BOLD returns a character vector giving the process identification numbers of the specimens found by the search.

  read.BOLD returns an object of class `DNAbin'. This object has the attributes "species", "accession_num", and "gene".

Warning

On 26 Oct 2011, attempts to access records using the eFetch system through a web browser resulted in an error, saying that eFetch and eSearch are offline for maintainance.

As of 7 March 2012, both functions have been modified to interface with the new BOLD architecture, and work as expected.

29 Oct 2012: It appears that BOLD has taken eFetch offline permanently, rendering read.BOLD as it currently stands useless. While we may be able to work out something, this will require a complete rewrite of the function. search.BOLD continues to work as intended.

17 Dec 2012: A new version of read.BOLD has been released that appears to work (for the time being).

Details

search.BOLD retrieves BOLD process identification numbers for any given taxon using the API for BOLD version 3.0. By default, it only returns the first 500 process IDs for the given taxon. By selecting the option exhaustive = TRUE, the function can be made to search for more than 500 process IDs, but is much slower.

stats.BOLD retrieves the total number of records for the given taxon.

read.BOLD downloads the sequences associated with the process identification numbers using a brute force method of downloading the specimen record, then searching and splitting the HTML code to remove the relevant information. This process is likely to make the function fairly unstable if BOLD make any changes to their website.

Previous versions of read.BOLD used the eFetch web service offered by BOLD to enable batch retrieval of records, however from October 2012 BOLD deprecated eFetch without providing a replacement service.

References

BOLD web services: http://services.boldsystems.org/.

BOLD version 3.0 http://v3.boldsystems.org/.

See Also

read.GB.

Examples

stats.BOLD("Pisauridae")

search.BOLD(c("Danio kyathit", "Dolomedes", "Sitona discoideus"))

nn <- search.BOLD("Pisauridae")
pisaurid <- read.BOLD(nn)

write.dna(pisaurid, "filename.fas", format="fasta")