How to import accession number (PMID) for a large number of references

Hej (Swedish),

I have started to use the accession number instead of therecord number when I paste a reference into a word document.


{Sepa, 2002, 12021156}
{Shahid, 2002, 12009297}

In the case of the Sepa reference, 12021156 is the accession number = PMID (Pumed ID).
However, I have discovered htat none of my references that were imported before year 2002 have any accession number (probably earlier versions of Endnote did not import accession numbers).

Is there a way I could import all lacking accesson numbers, or in some way synchronize the content of my current endnote references with the latest version of the pubmed references?

Or do I have to update all references without accession number manually?

Best regards, Dr Jonas F Ludvigsson, Sweden

I’m afraid the answer is “manually”.

Since your reference in your library doesn’t have unique identifier that links “back” to Pubmed, there isn’t an easy way. I realized this problem in the Pubmed (MEDLINE) import filter around version 8, and I made my custom filter that allows me to import Pubmed ID into my custom filed. Later, I moved the filed to Accession number. But I had to manually re-import several hundreds of reference with the custom filter. Now all of my reference has Pubmed ID, which you know, recent changes in NIH grant proposal mandate you to provide all the reference with Pubmed ID (is that the reason you use pubmed ID as identifier in Word?).

As to the manual re-import work, what I did was to create custom style that exports Author field with Doe J format (and export all authors), Journal title field, and the publication year, and separate them just with a space. Then, from Endnote, using Ctrl+K  which copies the formatted information to memory, I pasted into the search window in Pubmed. Unless the article is single-authored and the author publishes a lot in the same journal, I usually hit a single reference. Then re-imported the reference in Pubmed again to my library. The work screwed up links to my previous manuscript, but that was acceptable. It still took hours to re-import several hundreds, but the custom field helped to streamline, and later it paid off.

If you have several thousands of references without Pubmed ID, I have no solution but using “auto pilot” software that works at the OS level. Hope this comment helps.

Best regards, 

Hej (Swedish) Myoshigi,

thanks for the response.

My intention was actually not to submit a grant application to the NIH (although I have done that previously).

What do you mean by “autopilor” (you mean : manual human work, or??)?

Best, Jonas

Oh, there is a certain category of software that automates the job in the OS and across applications. It is sort of macros, like the macro in excel, except it works at OS level (Google Windows XP automation, to find out examples). But I have to write a “script” to automate the task I want. Say for example, type Ctrl+K in Endonote, switch to Explorer, find a reference in Pubmed, import it to Endnote…can be fully automated, if you have time to tweak the macro script. I tried some before, but my conclusion was always “if I spend this much of time to write macro automation script, manually doing each of them would be faster…”

If the number of references that doesn’t have pubmed ID is several hundreds, I believe re-importing may not be so bad.

Pubmed has “Clipboard” function, in which you can keep the references of interest up to 500 (for 8 hours).

From your Endnote library, just use the Ctrl+K export (with the format I mentioned in the previous post), go to Pubmed, Ctrl+V in the search window, and hit Go. Then, save the reference in the Clipboard (by choosing pull down menu of “Send To”). You repeat this “search and save” until you feel enough (say 50 or 100 references) is done. You can export all the references in the Clipboard with MEDLINE format, and import them to Endnote.

It’s not really elegant solution, but just in case you are interested in doing it, I attach the format I used.

Best regards,
Author Journal Year export for Pubmed Search.ens (5.69 KB)


I will do it manually.

Best, Jonas

Can you copy multiple lines in search window? I copied 8 lines in notepad, paste in search window in pubmed,only the first line is copied.

 Careful here - the PMID and PMCID numbers are different.  It’s the PMCID you want for NIH purposes.  See this link: