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7/1/2026

EndNote: What to watch out for when you're editing with EndNote

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"You shouldn't have any problems with the references  – we used EndNote"
This was the slightly optimistic comment that arrived with a large document that had, indeed, been referenced using EndNote. Now, although using EndNote for references does have many benefits, you won't be surprised to know that there are a variety of ways that errors can creep in. I'm going to tell you about some of the common problems that I've come across.

Why EndNote references sometimes go wrong

The two main reasons that EndNote references don't look the way they should are:
  • there is something wrong with the reference data in the EndNote library; and
  • something is not quite right with the EndNote output style.
If you have chosen to use an official EndNote output style (from here), the output style shouldn't be the problem, so the first place to look for problems is the EndNote library. You will probably find that, for one reason or the other, the reference data hasn't been added in correctly. I'll give you some examples of a few things that can go wrong.

Why don't the author names look quite right?

EndNote allows you to add author names in lists with no punctuation:
Billy Griffin
Katherine Gist

or as surname<comma> forename:
Griffin, Billy
Gist, Katherine

If the authors' surnames look suspiciously like forenames ...
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... you probably need to go and check where the commas have been put in the Author field.
In cases where the author is an organization, let EndNote know that the name should be written out as you've typed it by adding a comma after the full name.
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The authors of this study were actually the 'Halt-It Trial Collaborators' and this would need to entered into the EndNote library with a comma after 'Collaborators'.

WHy don't my References have the proper punctuation?

Selim M. Perioperative stroke N Engl J Med 2007 356 706–13 
This reference has all the details it needs, but it's missing the punctuation separating the elements in the reference. This can happen because extra spaces have been added at the end of each data field. Tidy up each field and make sure that only the necessary text has been added to each, and the punctuation will reappear!
Selim M. Perioperative stroke. N Engl J Med. 2007;356:706–13.

What happens when the type of reference hasn't been assigned correcly

This is an EndNote library entry for a journal article ...
Chai-Adisaksopha C, Hillis C, Siegal DM, Movilla R, Heddle N, Iorio A et al. Prothrombin complex concentrates versus fresh frozen plasma for warfarin reversal. A systematic review and meta-analysis. Thromb Haemost. 2016;116:879–90. doi: 10.1160/TH16-04-0266
You can see that all the elements you'd expect in a reference for a journal article are there (the doi has been entered further down the list of possible fields), and the type of reference has been correctly selected:
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References for books contain different elements so, if I change the Reference Type (circled in the image above) to 'Book', the reference ends up looking like this:​
Chai-Adisaksopha C, Hillis C, Siegal DM, Movilla R, Heddle N, Iorio A et al. Prothrombin complex concentrates versus fresh frozen plasma for warfarin reversal. A systematic review and meta-analysis; 2016 (https://www.ncbi.nlm.nih.gov/pubmed/27488143, accessed 27 October 2020).  
This reference appears odd because at first sight it appear as a book with missing publisher information. A quick look at the reference in the EndNote library shows the real problem.

What happens when EndNote library reference fields are not correctly filled in

I wasn't really sure what was going on with this reference:
Swartout WR. Rule-based expert systems: The mycin experiments of the stanford heuristic programming project: B.G. Buchanan and E.H. Shortliffe, (Addison-Wesley, Reading, MA, 1984); 702 pages, $40.50. Artificial Intelligence. 1985;26:364–6. doi: 10.1016/0004-3702(85)90067-0.
... but it turned out that the reason it looked so strange is that some extra, unwanted, information had somehow ended up being entered in the Title field of the EndNote library entry:
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What happens when data are Missing have been added to the wrong field

Other problems arise when, for some reason, the Endnote library reference doesn't contain all the data that is needed, or the data has been added to the wrong field.
Anand SS, Bosch J, Eikelboom JW, Connolly SJ, Diaz R, Widimsky P et al. Rivaroxaban with or without aspirin in patients with stable peripheral or carotid artery disease: an international, randomised, double-blind, placebo-controlled trial. 2018.
This journal article reference is missing all its publication details apart from the publication year. This sometimes happens when the author has referred to an article that hadn't been published when it was entered into the EndNote library and hadn't been updated since.
Shah AA, Haider AH, Riviello R, Zogg CK, Zafar SN, Latif A et al. Geriatric emergency general surgery: Survival and outcomes in a low-middle income country. Surgery. 2015. doi: 10.1016/j.surg.2015.03.045.
This reference is incomplete because the data in the EndNote library reference are in the wrong fields:
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Why are some titles in title case and some in sentence case?

References in bibliographies created by EndNote often have some references in sentence case and some in title case because of the way that EndNote deals with title capitalization.
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In each output style, EndNote provides three options, which you can find under 'Title Capitalization' in the 'Bibliography' settings in the output style editor:
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If you choose sentence case, EndNote does gives you the option of listing words that need to retain their capital letters (in the Edit/Perferences menu). I find that there are just too many words to list, and too many that might use a capital in one instance and not in the other, so I usually select 'Leave titles as entered' and change the case of each reference titles to suit the style I'm working with.

What do I do with those pesky Rogue references that I just can't correct?

Sometimes you've gone through the reference list, identified all the dodgy looking references, checked them, corrected their details ... and you still have a reference that isn't behaving properly in your list. This is often because EndNote is working with two libraries: the one you think you're working with, and the EndNote library that is embedded within the Word document. This second library is called the 'Traveling Library' and is very useful when authors add references to a document that you've sent back to them. You can see which library your references belong to in you click on 'Edit & Manage Citation(s)' on the EndNote tab. You will get a pop-up box that looks like this:
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You can update individual references by using the drop-down box on the right and select 'Update from My Library...' or export the travelling library into your library usign the 'Export to EndNote' drop-down box on the EndNote tab.
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Check for duplicates using 'Find Duplicates' in the Library menu in your EndNote library and update all citations and bibliography.


For other EndNote tips, see:
Using EndNote to style references in documents that don't use EndNote
What you need to edit documents that use EndNote
Using abbreviations for journal names in EndNote
Checking your document for reference management systems


Author

Andrea at Yours Truleigh Editing.
www.yourstruleighediting.com

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    Author

    Andrea at Yours Truleigh Editing
    I'm an editor based on the south coast of the United Kingdom. I use Word tools to make the editing process as effiicient and accurate as possible, and I'm hoping to share some of the tips and techniques I've picked up along the way. I'm an enthusiastic and grateful member of the Chartered Institute of Editing and Proofreading. Editorial freelancers benefit hugely from being part of supportive organizations:  for direct support for our work, such as training and providing routes for our clients to find us, but also for community, which is needed now more than ever. 
    Please note: all Word tips are based on Word 365 for PC. 

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