pubmed {annotate} | R Documentation

## 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=.pmfetch("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 pmfetch engine from the NCBI website.

### 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 type loop or you may find your access revoked.

### 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.

### Author(s)

R. Gentleman

### See Also

`genbank`, `xmlTreeParse`

### Examples

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

[Package annotate version 1.20.1 Index]