Skip to Main Content

The University of Otago Library has updated its Subject Guides system. Please let us know what you think by filling out this survey.

EndNote for Thesis Writers & Researchers

Manage your Library

Manage the content of your library

Check out the Organising your EndNote library section in the EndNote X9 guide that talks about working with Groups and getting comfortable with your EndNote library.

For larger projects, especially systematic reviews, there are additional things to consider:

  • You should absolutely always remove duplicates from your library before you start writing. However once the duplicate records are removed, your library can no longer be used to accurately report the 'where and when and how much' of what your searches retrieved. Think about having two EndNote libraries, one to hold and be the permanent record of everything you found, where you found it, and when; and a separate library that is the deduplicated and corrected version of the first library, which will be the one you will use for writing (see the Maintaining References section of the EndNote X9 guide).
  • If the topic you are working on is complex, or if you want to group your records in multiple ways, consider using unique keywords added to the Label field for counter-themes as an adjunct to groups and group sets, e.g.
    EndNote - Label field

Manage how you use your library in collaboration

Whether you are working with a supervisor (or supervisors), or with collaborators, you will need to think about how you share your EndNote library.

Using EndNote web, you can share your library with others, and you can choose to let them edit simultaneously, or you can restrict their access to read-only. Instructions for this are in The Little EndNote How-To Book, but there are caveats, so look at the whole section (Chapter 7, pp 84-104) before you start and raise any issues that occur to you with us.

The Little EndNote How-To Book cover

If you do not like the idea of sharing, you can always offer your library as a compressed or archived library. EndNote has its own zip software to optimise the process of combining the .enl and .Data files of your library, which you can find in the File menu.

You can choose whether or not to include the attached PDFs which may make even a zipped file heavy (remember to check the terms and conditions for each PDF you share with someone outside the University of Otago), and whether to send all or part of the library.

The resulting compressed file will have a .enlx suffix, and will be called an Archived EndNote library.

EndNote - library share menus

Submitting chapters or interim work to your supervisor

If you need to submit chapters to your supervisor, and you want to use Track Changes, agree on a format with your supervisor that will keep what you write as safe as possible (see section on Issues with code.)
We do not recommend sending an EndNote-rich document for review if Track Changes are to be used.

Option one:
If your supervisor wants to see what you have written in a format as close as possible to the finished work, you may choose to submit what you have written as plain text, and transfer suggestions across to your EndNote-rich document later. This is the safest option, and poses the least risk of corrupting your EndNote references. Please see the section on Before Submitting in the EndNote X9 Beginner's guide.

Option two:
An alternative is to use a document with unformatted citations, and create a reference list that you can copy and paste onto the end. Your submitted document will look something like this:
This option is safe, and poses a low risk of your references being corrupted. This works better with author-date styles (such as APA) than with numbered styles (such as Vancouver).
To do this:

  • First, save a back-up copy of your document.
  • In the EndNote toolbar in Word, select Convert Citations and Bibliography, and click Convert to Unformatted Citations.
  • As you enter references into Word, EndNote creates a temporary folder to show what you have used. You can use the content of this folder to create a reference list for a document with unformatted citations.
    • Ensure you have the correct referencing style selected from the style drop-down menu.
    • Highlight all of the references in the temporary folder in EndNote.
    • Right-click, and select Copy Formatted.
    • Paste the references into your Word document wherever you want your reference list to be.

These options can both be fiddly to start with, but become more straightforward with experience. Please do not hesitate to contact us if you would like help with the process.