pm.getabst {annotate} | R Documentation

## Obtain the abstracts for a set PubMed list.

### Description

The data provided by PubMed is reduced to a small set. This set is then suitable for further rendering.

### Usage

    pm.getabst(geneids, basename)

### Arguments

`geneids` | The identifiers used to find Abstracts
`basename` | The base name of the annotation package to use.

### Details

We rely on the annotation in the package associated with the `basename` to provide PubMed identifiers for the genes described by the gene identifiers. With these in hand we then use the `pmfetch` utility to download the PubMed abstracts in XML form. These are then translated (transformed) to a shorter version containing a small subset of the data provided by PubMed.

This function has the side effect of creating an environment in `.GlobalEnv` that contains the mapping for the requested data. This is done for efficiency – so we don't continually read in the data when there are many different queries to be performed.

### Value

A list of lists containing objects of class `pubMedAbst`. There will be one element of the list for each identifier. Each of these elements is a list containing one abstract (of class `pubMedAbst` for each PubMed identifier associated with the gene identifier.

### Author(s)

Robert Gentleman

### See Also

`pm.abstGrep`, `pm.titles`

### Examples

    hoxa9 <- "37809_at"
       ## A bit of a hack to not have a package dependency on hgu95av2
       ## but need to fiddle w/ the warn level to not fail the example anyways.
       curWarn <- getOption("warn")
       options(warn=0)
       on.exit(options(warn=curWarn), add=TRUE)

    if( require(hgu95av2) )
        absts <- pm.getabst(hoxa9, "hgu95av2")

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