It works like a charm if my filtered vector contains less than 300 pmids but, as also other people mentioned it exits with an error when exceeds that limit:
Error in entrez_check(response) :
HTTP failure 414, the request is too large. For large requests, try using web history as described in the rentrez tutorial
I have tried splitting into chunks e.g. http://www.nagraj.net/notes/chunking
but my problem here is that I need one parsed xml file to extract the information and splitting or merging parsed xmls did not seem to work for me.
I would appreciate any ideas about fixing that issue.
Hi!
I am quite troubled with big queries in pubmed.
The problem is as follows: I try to use entrez_fetch to extract parsed xml file as I need it to extract abstracts and mesh terms from pubmed.
fetch.pubmed <- entrez_fetch(db = "pubmed", id = filtered, rettype = "xml", parsed = T)It works like a charm if my filtered vector contains less than 300 pmids but, as also other people mentioned it exits with an error when exceeds that limit:
Error in entrez_check(response) : HTTP failure 414, the request is too large. For large requests, try using web history as described in the rentrez tutorial
I have tried splitting into chunks e.g. http://www.nagraj.net/notes/chunking but my problem here is that I need one parsed xml file to extract the information and splitting or merging parsed xmls did not seem to work for me. I would appreciate any ideas about fixing that issue.
Thank you in advance Thodoros