pubmed: A function to open the browser to Pubmed with the selected gene.

Description

Given a vector of Pubmed identifiers or accession numbers, the user can either have a browser display a URL showing a Pubmed query for those identifiers, or a XMLdoc object with the same data.

Usage

pubmed(...,disp=c("data","browser"), type=c("uid","accession"), pmaddress=.efetch("PubMed", disp, type))

Arguments

...

Vectorized set of Pubmed ID's

disp

Either "Data" or "Browser" (default is data). Data returns a XMLDoc, while Browser will display information in the user's browser.

type

Denotes whether the arguments are accession numbers or UIDS. Defaults to uids.

pmaddress

Specific path to the pubmed efetch engine from the NCBI website.

Value

If the option "data" is used, an object of type XMLDoc is returned, unless there was an error with the query in which case an object of type try-error is returned.If the option "browser" is used, nothing is returned.

Details

A simple function to retrieve Pubmed data given a specific ID, either through XML or through a web browser. This function will accept either pubmed accession numbers or NCBI UIDs (defined as a Pubmed ID or a Medline ID) - although the types must not be mixed in a single call.

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 tight loop or you may find your access revoked.

Examples

Run this code

   if( interactive() )
    opts <- c("data","browser") else
    opts <- "data"
   for (dp in opts)
     pubmed("11780146","11886385","11884611",disp=dp)

Run the code above in your browser using DataLab

Data engineering and BI courses are free!