accessionToUID: A function to convert accession values to NCBI UIDs.

In Bioconductor/annotate: Annotation for microarrays

A function to convert accession values to NCBI UIDs.

Description

Given one or more accession values, this function will attempt to convert them into NCBI UID values.

Usage

accessionToUID(...,db=c("genbank","pubmed"))

Arguments

...	Accession numbers to be transformed.
db	Which database this accession number refers to, defaults to Genbank

Details

Utilizes the PubMed tool esearch.fcgi to convert an accession number into a valid NCBI UID number.

WARNING: The powers that be at NCBI have been known to ban the IP addresses of users who abuse their servers (currently defined as less then 2 seconds between queries). Do NOT put this function in a type loop or you may find your access revoked.

Value

Returns either a valid NCBI UID value or NULL (if there was nothing available).

Author(s)

Jeff Gentry

See Also

pubmed, xmlTreeParse

Examples

     ## The two returns from genbank should be the same
     xdoc <- genbank("U03397",type="accession",disp="data")
     x <- accessionToUID("U03397",db="genbank")
     xdoc <- genbank(x, type="uid",disp="data")

     ## Can handle multiple inputs
     y <- accessionToUID("M16653","U892893",db="genbank")

Bioconductor/annotate documentation built on Nov. 2, 2024, 4:40 p.m.