Conjunction and disjunction in pubmed query
On Dec 27, 2012, at 3:10 PM, email wrote:
Hi: I am trying to query pubmed abstracts using the following syntax: url= "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" search = paste(url, "db=pubmed&term=", queryTerm1, "+AND+", queryTerm2,"+OR+",queryTerm3, "+OR+", queryTerm4, "[abstract]&retmax=100&usehistory=y", sep="")
I get an error here: Error in paste(url, "db=pubmed&term=", queryTerm1, "+AND+", queryTerm2, : object 'queryTerm1' not found
docId <- xmlTreeParse(getURL(paste(url, search, sep="")), useInternalNodes=TRUE) I want to fetch abstracts containing queryTerm1 AND queryTerm2 Or queryTerm3 OR queryTerm4. The code runs without error, but from the result I find that conjunction and disjunction is not working.
"Not working" is a phrase that conveys very little. What exactly are you seeing, and how is it different than what you expected to see.
Can anyone suggest a correct syntax for doing AND and OR pubmed query?
Reviewing an earlier question [Subject: Re: [R] query multiple terms in PubMed abstract Date: December 11, 2012] I find that you did not reply to my earlier response where I said your code was returning expected results and asked what problems were prompting your questions. If you do not respond to questions and fail to include complete code, there is little people will be able to do. You need to provide complete code and a more complete problem description. If I were interested in articles the had MeSH headings for "mortality" and "leukemia" I would first attempt constructing a search phrase that looked like "mortality[mh] AND leukemia[mh]" rather than "mortality[mh]+AND+leukemia[mh]". But I see that the "+" symbol seemed to succeed last time. You may need to use parentheses to get the intended grouping of PubMed search expressions.
David Winsemius, MD Alameda, CA, USA