pm.getabst {annotate}R Documentation

Obtain the abstracts for a set PubMed list.


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


pm.getabst(geneids, basename)


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


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.


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.


Robert Gentleman

See Also

pm.abstGrep, pm.titles


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")
   on.exit(options(warn=curWarn), add=TRUE)

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

[Package annotate version 1.8.0 Index]