R help - Dec 2012 - query multiple terms in PubMed abstract

Hi:

I am trying to search PubMed abstracts which contains BOTH two terms:
COL4A1 AND Ocular. I am using the following code:

url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
search = paste(url,
"db=pubmed&term=COL4A1+AND+Ocular[abstract]&retmax=300",
sep="")
docId <- xmlTreeParse(getURL(paste(url, search, sep="")),
useInternalNodes=TRUE)


I want to get the reply where BOTH the terms exist in abstract. But it is
not doing that now. Any idea?

Thanks
john

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On Dec 11, 2012, at 6:42 AM, email wrote:
> Hi:
>
> I am trying to search PubMed abstracts which contains BOTH two terms:
> COL4A1 AND Ocular. I am using the following code:
>
> url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?"
> search = paste(url,
> "db=pubmed&term=COL4A1+AND+Ocular[abstract]&retmax=300",
sep="")
> docId <- xmlTreeParse(getURL(paste(url, search, sep="")),
> useInternalNodes=TRUE)
>
>
> I want to get the reply where BOTH the terms exist in abstract. But  
> it is
> not doing that now. Any idea?
When I first load packages XML and RCurl, a step which you did not  
mention, and then use the "search" url that was constructed by that  
paste operation in a browser I get an XML output suggesting successful  
construction of a valid search. Checking against an ordinary search it  
appears that you were successful in forming a proper conjunction in  
the Pubmed search syntax.

I then wondered what your problem really was. You never really stated  
whether you were experiencing errors or not getting the correct Pubmed  
IDs or were having difficulties understanding the output.

-- 
David Winsemius, MD
Alameda, CA, USA