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Science, Agriculture and Engineering Postgraduate Researcher Development Programme: Workshop 5: Advanced EndNote

Materials to support the SAgE Postgraduate Researcher Development Library workshop Programme

Workshop overview

This workshop is aimed at those experienced in using EndNote, who would like to learn more about how the software can help in the writing up stages of a PhD. In this workshop, you will learn more about the advanced features of EndNote, including how to: 

 Manage long documents

 Share documents and/or EndNote libraries with your supervisor/research group

 Write for publication using manuscript templates, term lists and journal styles

Combining Word documents and bibliographies

If you are working on a long document, such as a dissertation or thesis, you may have several chapter documents which you wish to combine into one. In this final document you may require chapter bibliographies, one final bibliography or both. To ensure your final document displays your references correctly you must be careful to unformat/reformat your documents correctly. Follow the appropriate instructions below.

To combine multiple Word documents into one with one final bibliography

  • Open each chapter document and in the EndNote tab of each click on Convert Citations and Bibliography > Convert to Unformatted Citations
  • Copy and paste your documents together into one final document
  • Ensuring that your corresponding EndNote library or libraries are open, in this final document click on Update Citations and Bibliography

Your document will be reformatted in your chosen style and will display one final bibliography at the end.

To combine multiple Word documents into one with chapter bibliographies

Keep each chapter document separate until the very end when you no longer wish to make any changes to your EndNote references. You will be combining them for printing/submission purposes only.

  • Open each chapter document and in the EndNote tab of each click on Convert Citations and Bibliography > Convert to Plain Text
  • You will be warned that this will create a new copy of your document stripped of all EndNote markers. Click on OK to continue
  • Copy and paste your documents together into one final document

Your final document will retain chapter bibliographies.

To create a separate bibliography

To create a separate bibliography document you need one EndNote library or group which contains all of the references you have used throughout your disseration or thesis but no more.

  • Ensure the correct referencing style is chosen within EndNote
  • Highlight all the references in your library or group as appropriate
  • Right click and select Copy Formatted
  • Open a blank Word document and paste the references into it

This document will display your full bibliography in your chosen style and can be added to the end of your submission.

Creating an EndNote library from a Word document

It is possible to create a new EndNote library from a Word document if the references in the document were originally inserted from EndNote. This feature will not work with plain text. It is useful if you have worked on a document using several EndNote libraries and you now wish to have a library which includes every reference you have used in your document and no others. You can easily create a separate final bibliography from such a library.

  • In Word, on the EndNote tab, click on Export to EndNote > Export Travelling Library
  • You get the option to export to an existing library or to a new EndNote library. Choose New and click OK
  • Give your new library a name and save it in a suitable location within your personal filespace (H drive)
  • You will be notified on screen that the Export is complete and your new library will show your exported references

Using abbreviated titles (terms lists)

If you need to use an abbreviated journal title as part of your referencing style you can import a journal terms list (list of standard abbreviations for journal titles) for use in your EndNote library.

  • Click on Tools > Define Terms Lists
  • Select the Journals term list then click Import List
  • Go to C:\Program Files (x86)\EndNote X7\Terms Lists, select the term list file appropriate to your subject area and click Open
  • Click on OK

The terms will be imported into the Journals term list. Click the Terms tab to view the enlarged Journals term list. Note that official abbreviations are included (Abbreviation 1: with punctuation, Abbreviation 2: without punctuation). Close the Term List box.

Some styles are set to use a standard abbreviation e.g. Royal Society of Chemistry which uses Abbreviation 1.

You can edit a style to use an abbreviated journal title by going to Edit > Output Styles > Edit [style name] > Journal Names and selecting the correct format from the list. Save the changes to the style and rename it - you will find it available to use in the Style Manager.

Writing for publication

If you're submitting a document for publication, you should remove the field codes which may be incompatible with a publisher's design software: Convert Citations and Bibliography > Convert to Plain Text.
WARNING: This strips your document of EndNote coding so is only advisable when you have completely finished editing the document.
Manuscript templates

See the EndNote website for downloadable templates.

Importing a single folder of PDFs

If you Have a folder of existing PDFs, you can import them into EndNote and EndNote will create references from them if possible.

  • Go to File > Import > Folder
  • Use the Choose button to navigate to the appropriate folder and click on OK
  • Ensure the Import Option is set to PDF and click on Import

If you have a large number of PDFs the import process may take some time.

Please note this feature is dependent on each PDF including full DOI information.  However, you can look up DOI information on the Crossref website here, which if you add manually to your reference, then click on the 'find full text' icon, may help import the full reference information.

Where the process has been successful you will see your PDFs attached to automatically-generated references. Where the process hasn't worked (as in the top reference pictured below) your PDF will be attached to an empty record. You will need to double-click to open this record and type in the details manually.

Importing multiple PDFs

EndNote Web - troubleshooting

EndNote Web allows you to synchronise your web-based library with your desktop version of EndNote. However, you can only synchronise ONE desktop EndNote library with your EndNote Web account.

If you have several EndNote libraries we recommend merging them into one master library and using the Groups feature to organise your references.

Using Endnote in a Group

Download this guide to using EndNote in a group and sharing libraries using EndNote Web.

Editing/deleting citations

Always use Edit & Manage Citations rather than the editing and/or deleting citations/references directly. This will ensure that the changes you make are saved.

Merging libraries

If you're looking to merge all or parts of two different libraries, EndNote allows you to do this easily. To see both libraries simultaneously:

Windows > Tile Vertically

You can then either drop and drag references or copy/cut and paste.


We recommend that you have one EndNote library for all your references and use the Groups feature to organise your references as needed.

Click on Groups > Create Group and label as appropriate.

This feature allows you to create mini libraries within your master library. You can add references to your newly created groups by highlighting single or multiple references and either dragging them to the group in the left-hand menu or selecting Groups > Add references to [Group Name].

You can also set up Smart Groups which automatically group references by set criteria (e.g. keyword).

Capturing references using the Bookmarklet Tool

The EndNote Bookmarklet Tool scans the bibliographic information presented on a webpage and creates a reference which you can save in either EndNote online or EndNote desktop. This is a particularly useful tool for those journal sites or webpages which do not offer a direct export option on screen.

For step by step instructions download the EndNote White Paper for free from Adept Scientific here (registration required). Capture Reference


Warning: Multiple authors will be listed on one line - after you've imported your captured reference(s) you'll need to edit the author field and ensure each name is on a separate line and displays correctly (either first name last name OR last name, first name). Also, ensure the Reference Type has been picked up correctly - you can change this before you import or afterwards.

What's new in EndNote X6?