search for: efetch

Hi, I want to use reutils to obtain the accession numbers of a query search in character format. When I use efetch, the accession number isn't in a character format, and I'm not sure if the number is accurate, because I get the error: Error in file.exists(destfile) : object 'destfile' not found This is what I tried: UIDs<-esearch( "Methylation" ) accession_numbers = efetch(UIDs,...

Hello! I am trying to get specific fields from an XML document and I am totally puzzled. I hope someone can help me. # URL URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" # download a XML file tmp <- xmlTreeParse(URL, isURL = TRUE) tmp <- xmlRoot(tmp) Now I want to extract only node 'pubdate' and its children, but I don't know how to do that unless I try to...

I would like to track in which journals articles about a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse("

...> print(node) > ) Gorjanc Gregor wrote: > Hello! > > I am trying to get specific fields from an XML document and I am totally > puzzled. I hope someone can help me. > > # URL > URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" > # download a XML file > tmp <- xmlTreeParse(URL, isURL = TRUE) > tmp <- xmlRoot(tmp) > > Now I want to extract only node 'pubdate' and its children, but I don't > know h...