[BioC] Trouble querying pubmed on strings

[Ken Termiso]

hi all,

i'm trying to get a function working that queries pubmed with any string and 
returns pubMedAbst objects corrresponding to the pubmed article hits from 
the query string...

this is my code so far, based partly from annotate's 'query.pdf' and also 
from the perl script from NCBI at 
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html :



library(annotate)
library(XML)

query <- "trk"

pmSrch <- function(query)
{
    utils <- "http://www.ncbi.nlm.nih.gov/entrez/eutils"

    esearch <- paste(utils, "/esearch.fcgi?" , 
"report=xml&mode=text&tool=bioconductor&", 
"db=Pubmed&retmax=1&usehistory=y&term=", query)
    esearch <- gsub(" ", "", esearch)
    cat(esearch, "\n")
    #return(esearch)   # returns URL

    return(.handleXML(esearch))
}

pms <- pmSrch(query)

a <- xmlRoot(pms)
numAbst <- length(xmlChildren(a))
numAbst
arts <- vector("list", length = numAbst)
absts <- rep(NA, numAbst)

for (i in 1:numAbst) {
arts[[i]] <- buildPubMedAbst(a[[i]])
absts[i] <- abstText(arts[[i]])
}


i don't know perl and i end up with numAbst = 8 (regardless of the search 
string) and esearch = 
http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?report=xml&mode=text&tool=bioconductor&db=Pubmed&retmax=1&usehistory=y&term=trk
but typing :

>arts[1]
[[1]]
An object of class 'pubMedAbst':
Title: No Title Provided
PMID: No PMID Provided
Authors: No Author Information Provided
Journal: No Journal Provided
Date: Month Year


simply gives me empty objects...

i'd appreciate any help anyone can give. i am not familiar with XML...

thanks in advance,
ken