Hi all,
Foreword: I'm incredibly inexperienced with R, Entrez et similia, but here I go.
I have noticed that on this website there is one answer to my question, unfortunately, I could not find it very helpful as it was too advanced for me. Specifically, you may find the answer here: Convert article title to pubmed ID
I am trying to get to a list of PMIDs from a list of Pubmed titles. I have learned that people query the Pubmed Entrez system through Reutils, or other tools, that are R compilers (forgive me if my terminology is off, I'm quite new).
This is what I am doing (it is only 1 out of 820 other papers!):
query_text = '"Markov models in medical decision making: practical guide[Title]"' esearch(query_text, db="pubmed")
Unfortunately, the result is:
Warning(s): PhraseIgnored in QuotedPhraseNotFound "Markov models in medical decision making: practical guide[Title]" Object of class ‘esearch’ PhraseIgnored "in" QuotedPhraseNotFound "\"Markov models in medical decision making: practical guide[Title]\""
I expect 1 pubmed ID. The reason (might be wrong) is that if I enter the text between quotation marks in the Pubmed query builder, it returns exactly 1 entry.
I would appreciate any help you can give me and wish you a pleasant weekend! :)
And using some bash-fu and loops you could easily do this for many more papers. Let us know if you can't get that working!
Hey!
Thank you for this reply.
I'm a Windows user, so I installed the Cygwin tool for running eutils, following the guide on the link you provided. I'm afraid that the same technical ignorance applies here, while earlier it concerned R, now it concerns Perl! For some reason, Cygwin will not perform any esearch, it just gets stuck.
I realize this is not a technical support forum for Cygwin, so I will try to solve this issue within my range of capabilities :) but thanks again for the input. I simply wonder why the R query does not work.
All the best
Hi I made a loop to convert the papers' titles to PMID, but I got the following errors:
nquire -url https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ esearch.fcgi -retmax 0 -usehistory y -db pubmed -term "NOD2 and bacterial recognition as therapeutic targets for Crohn’s disease[title]" -tool edirect -edirect 17.4 -edirect_os Linux -email apple@gearshift <?xml version="1.0" encoding="UTF-8" ?> <!DOCTYPE eSearchResult>
<eSearchResult> <ERROR>Empty term and query_key - nothing todo</ERROR> </eSearchResult> QUERY FAILURE
Is there any ways to deal with that ?
Looks like there seems to be a problem with EntrezDirect. Please put a ticket in with NCBI Help desk and let them know.
Update: Seems to work for me.