Here is a problem you might come across as a copy-editor or co-author of an academic paper. You want to format the references in a paper in Word format, but you just have a bunch of PubMed IDs. No problem, it’s possible with EndNote! For this demonstration, I used EndNote X9 and Office 365 for Windows.

Screenshot of a Word document showing a paper with PubMed IDs in brackets in place of references

The first step is to extract all of the references from the document, and add them to a list. I’m sure there’s an easier way to do this (maybe using macros), but I just used the search function. You can search for longer numbers with an open bracket in front of them, like this: (^#^#^#^# .

In EndNote, you can do an online search for references using PubMed. To do this, you can use the “Online Search…” function (which is in the toolbar), and then select the EndNote database. You can copy and past the list of references across.

Screenshot of EndNote, showing the Online Search function on the toolbar
Screenshot of EndNote's online search function

These can then be copied to your local library with the function “Copy to Local Library”.

Screenshot of EndNote, showing the online search and the Copy to Local Library function

The next step is then to replace the brackets with curly brackets {}, so that EndNote will actually recognise them as unformatted references. Once this is done, you can turn Instant Formatting on. EndNote will work through them and match them with the newly created references in your EndNote local library. (Unfortunately, it cannot search PubMed to find missing references at this stage. If they’re not in your local library, it doesn’t know about them.)

Note that you will need to work through these. EndNote will ask you to confirm each reference, which might take a while for a longer document with many references.

Screenshot of a Word document showing a paper with PubMed IDs in brackets in place of references in curly brackets

Et voilà! You should now have perfectly formatted references in place of the PubMed IDs.

Screenshot of a Word document showing a paper with formatted references

As always, if you need help with copy-editing and formatting, you can always contact me. I offer a reliable service and competitive rates!


I am a student of oenology, botany, and TESOL. I am also a photographer. You can find out more about me here:


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