Pubmed title to pubmed ID conversion

Question

[daniele.sartori01]

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! :)

Answer 1

[GenoMax]

You can use NCBI command line eutils to do this. Using the example you posted above esearch -db pubmed -query "Markov models in medical decision making: practical guide" | efetch -format native generates

1. Med Decis Making. 1993 Oct-Dec;13(4):322-38.

Markov models in medical decision making: a practical guide.

Sonnenberg FA(1), Beck JR.

Author information: 
(1)Department of Medicine, UMDNJ Robert Wood Johnson Medical School, New
Brunswick 08903.

[text deleted to save space]

PMID: 8246705  [PubMed - indexed for MEDLINE]

or you could simply do

esearch -db pubmed -query "Markov models in medical decision making: practical guide" | efetch -format native | grep PMID to get this

PMID: 8246705  [PubMed - indexed for MEDLINE]

[WouterDeCoster]

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!

[daniele.sartori01]

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

[baijingjing2018]

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 ?

[GenoMax]

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.

$ esearch -db pubmed -query "NOD2 and bacterial recognition as therapeutic targets for Crohn's disease [TITLE]" |  efetch -format native | grep PMID 
PMID: 29096557  [Indexed for MEDLINE]