pmAbst2HTML {annotate}R Documentation

HTML Generation for PubMed Abstracts


This function will take a pubMedAbst object, or a list of these objects and generate a web page that will list the titles of the abstracts and link to their full page on PubMed


pmAbst2HTML(absts, filename, title, frames = FALSE, = TRUE)


absts A list of pubMedAbst (or a single object)
filename The output filename. If frames is FALSE, this is the name of the single output file and defaults to absts.html. Otherwise, this is taken to be the base of a set of filenames, and the default base is the empty string. See value for more information on output files.
title Extra title information for your listing
frames If frames is TRUE, the resulting page will use HTML frames, resulting in a more complex set of output pages. If TRUE, will center the listing of abstracts


This function uses the Entrez functionality provided by NCBI to retrieve the abstract URL at the PubMed site. It will then create a tabular webpage which will list the titles of the abstracts provided and have them link to the appropriate PubMed page. If frames is TRUE, the table of links will be on the left hand side of the page and the right hand will link directly to the appropriate PubMed page.


If frames is FALSE, a simple HTML file is created with the name specified by filename.
If frames is TRUE, then there are four HTML files created, of the form XXXtop.html, XXXside.html, XXXmain.html and XXXindex.html, where XXX is the string provided by filename.


This function is part of the Bioconductor project at the Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R


Jeff Gentry

See Also



        x <- pubmed("9695952","8325638","8422497")
        a <- xmlRoot(x)
        numAbst <- length(xmlChildren(a))
        absts <- list()
        for (i in 1:numAbst) {
           absts[[i]] <- buildPubMedAbst(a[[i]])
        ## First try it w/o frames - using a temporary
        ## file for the output
        fname <- tempfile()

        if (interactive())

        ## Now try it w/ frames, using temporary files again.
        fnameBase <- tempfile()
        pmAbst2HTML(absts,filename=fnameBase, frames=TRUE)

        if (interactive())

[Package annotate version 1.8.0 Index]