EndNote FAQ Top 10

This problem often occurs if the .enl file and the .data file folder are not saved in the same folder at the same location.

  • In File Explorer, find their location in Athena and put them together again.
  • Tip: In your H-drive create a new folder called EndNote in which to save all your EndNote files, specifically your library and all your PDFs with full text. This will make it easier to find them, and the .enl file and the .data file folder will remain together.
  • Open EndNote, Word and Internet Explorer via Athena so that you can make full use of all the functionalities.
  • Via File Explorer go into Athena and find the .enl file and the .data file folder of your library via ‘Search in home’ (see screenshot).
  • Double-click on the .enl file to open your library or select File > Open Library in EndNote.

TIP: In your H-drive create a new folder called EndNote in which you can save all your EndNote files, specifically your library and all your PDFs with full text. This will make them easier to find. It is important that you keep the .enl file and the .data file folder together.

For an automatic import, you need to open both EndNote and your browser via Athena.

There are two options:

  1. (preferred option) Close the database(s) in your browser and open them again in a browser via Athena. Forget the downloaded file and start again with the automatic import.
  2. Use the Import button in EndNote to import the downloaded file again (usually in RIS format) into EndNote.

N.B.: If you choose this option, you will have to indicate an import option compatible with your database. If you do this incorrectly, the import will fail.

EndNote Online is the free version with limited functionalities. They may also be referred to as EndNote Basic and EndNote Web. You can access them via this link

UGent pays a licence fee for the Desktop version for all personnel and students. This version offers all functionalities, including more storage capacity. You will find EndNote Desktop on the Athena platform.

N.B.: If you want to share libraries via the Desktop version, you first have to create a free EndNote online account.

Tip: In order to transfer your references from EndNote Online to EndNote Desktop:

  • In EndNote Online: under menu Format: Export References > EndNote Export as style
  • In EndNote Desktop: File > Import > format EndNote Import

While writing, you can add your citations with the Cite While You Write function in Word and create your reference list based on your EndNote library. Select your output style in the EndNote tab in Word.

APA style

This is a name-year system. The citations look like this:  ([Author(s) surname], [year]).

In the reference list your references are ranked alphabetically by surname of the (first) author. Anonymous references appear at the top.

Vancouver style

This is a numerical system. In the text your citations consist of Arabic numerals that refer to the order in which the reference is first mentioned in the text.

In the reference list, your references are ranked in ascending numerical order.


  • In the EndNote tab in Word, select the correct style.
  • The reference list and the citations are automatically changed to the requested style.

For example: {Bracke, 2010 #12;Huvenne, 2010 #14;Pauwels, 2014 #3}

  • Go to the EndNote tab in Word (see screenshot).
  • Click on Update Citations and Bibliography to apply the formatting again.

There are 2 ways to add your PDFs to your library.

  1. Automatically
  • Select the references for which you want to import the full text and click on Find Full Text (see image).
  • In the left column, the temporary group Find Full Text appears, and you can follow the progress of the search in the databases to which EndNote has access.
  • The PDFs are automatically linked (indicated with a paperclip in the list with references) and appear in the PDF Preview window when you select the reference.

2. Manually

Due to authentication processes, EndNote does not have access to all the PDFs that UGent accounts can access via the SFX button. You will therefore have to add some of them manually.

  • Download your PDFs and save them in your H-drive. Tip: create a subfolder in your EndNote folder.
  • Click on Attach File (paperclip) and link your PDF to the relevant reference.
  • Open the EndNote tab (in Word) and click on Select Another Style.
  • You will have access to thousands of output styles to choose from.
  • If you can’t find the style required by the guidelines, then check this page
  • Download this on your PC at the same location as the other styles.

TIP: the location of the reference styles can be found as follows: Edit > Preferences > Folder Locations

Comment: Make sure that you always select and change your reference style in Word not in EndNote.

If you can’t find the appropriate reference style (see steps in question 8) or there is not a 100% match, then you can manually change the output style in EndNote.

  • Edit > Output Style > Edit Style ‘X’ or Open Style Manager > Select a reference style > Edit.
  • Always save your changes under a different name (File > Save As)!
  • Make your changes under Citations > Templates (for citations in your text) and/or under Bibliography > Templates (for your reference list).
  • Make sure you use the exact syntax for your changes. For example, you can copy/paste the exact notation of an item that has to be changed from a different sort of reference type.
  • And don’t forget to tick the changed output style in your Word file (see question 7).
  • If you haven’t done so already, create an EndNote Online account.
  • Make a back-up of your EndNote Desktop library (see also question How do I make a back-up of my library? in the section FAQ other questions).
  • Click on Sync (see screenshot) thus allowing your library in EndNote Desktop to synchronise with your library in EndNote Online. You can also share just one group from your library.
  • Click on Share and enter the e-mail addresses of those with whom you want to share your library. Select ‘Read Only’ or ‘Read & Write’.
  • If you don’t want to share your entire library, select the group from your references in your EndNote Online account: Organize > Manage My Groups.


In the synchronisation process, your EndNote Desktop library and your EndNote Online library will be merged. If you have other references in your Online version, you should first remove them and/or save them elsewhere.

! Make sure that automatic synchronisation cannot take place until the 1st synchronisation is complete.

  • Click on Edit > Preferences > Sync in the men
  • Untick the box Sync Automatically

FAQ other

There is more information about this on the KCGG website at this link.

  • Click on Edit > Preferences > Reference Types > Modify Reference Types
  • Add new fields in the Custom (1,2, etc.) fields (see screenshot). The best option is to choose a field that has not yet been filled in by EndNote for a certain Reference Type (e.g. Custom 3 in the case of a Journal Article)
  • In order to make the personalised fields visible:

click on Edit > Preferences > Display Fields (see screenshot).

Duplicate references can be deleted all together in one click or manually one by one.

  1. Manually
  • Go to References > Find Duplicates
  • Click on Keep This Record in order to save the correct of the two references. Click on Skip to keep both versions.

2. All at once

  • Go to References > Find Duplicates > click on Cancel.
  • The temporary group Duplicate References appears in the left-hand column.
  • Go back to the group in which the duplicates were traced. There you will see all double references highlighted in blue or light grey.
  • Right-click on one of the highlighted references > select Remove References from Group.


Errors can occur both in the manual and one-click removal of all duplicates.

  • False positive results: references are incorrectly indicated as duplicates (e.g. conference abstract with same title as article, commentaries, corrections).
  • False negative results: references are not indicated as duplicates when they are (e.g. minor difference in way title or author’s name is written).


Remove a number of fields on which the comparison between possible duplicate records is based.

Go to Edit > Preferences >Duplicates > untick Author and Reference Type as required fields.

You can then check these fields manually per record, by making them visible via Edit > Preferences > Display Fields (tick Author and Reference Type)

There are two options.

  1. Separate files.
  • Copy both files from your library: your .enl file and the accompanying .data-folder.
  • Save them elsewhere, but keep them together.

2. Compressed folder

  • Click on File > Compressed Library > Save this compressed folder elsewhere.
  • All data are now housed in one file with an .enlx

Tip: you can send this Compressed Library by e-mail

  • Click on Tools > Change or Move/Copy Fields > Select a field
  • You can now change your fields, for example by adding a keyword to a set of references or mentioning the database.

On the basis of the DOI of an article EndNote can search  for a PDF that matches the information in your references.

  • Check if you have already created a (sub)folder in your H-drive where you keep all your PDFs with full text. Do this under your EndNote folder.
  • Click on Edit > Preferences > PDF Handling
  • Tick the box Enable automatic importing under PDF Auto Import Folder (see screenshot)
  • Then select the (sub)folder in which you have saved all your PDF full text files in your H-drive.

Automatic import

  • Check if the Medical Journal Term List is imported in your EndNote file.

Click on Lists > Journals > Import List > Open Medical.txt

  • Check if the chosen Output Style is configured for the use of abbreviations instead of the full name of the journal.
  • Click on Edit > Output Styles > Edit “ X “ > Journal Names
  • Tick Abbreviation 1 for an abbreviation style with periods

OR tick abbreviation 2 for an abbreviation style without periods.

TIP 1: Save the original Output Style and save your changes under a different name.

TIP 2:

If you didn’t import the Medical Term List when you first created your library, it may be that, after importing that list, a certain journal appears there twice. EndNote will then be unable to use the correct abbreviation and you will have to delete and/or manually change one of them.

  • Click on Tools > Open Term Lists > Journal Terms List > tab Terms > Update List. Manually change the abbreviation.
  • Delete any duplicates in the same way.

You can share a limited reference library using a Travelling Library.

  • In Word go to the tab EndNote > Export to EndNote
  • Export Travelling Library > A new Endnote Library and save.

TIP: If you are sent a Word file by someone else with references that are not yet included in your personal EndNote library, you can import these too, by following the same steps as above (Export Travelling Library), but click on An Existing EndNote Library.

Temporary groups contain references that you have recently created or imported. After closing your EndNote library, or after a new search query, this temporary group is deleted. For example: import of references from an external database (see Imported References group); online search from EndNote.

Permanent groups: The other groups remain unchanged after closing and re-opening your EndNote library. For example: All References, Trash, Unfiled references, Group(sets) or Smart Groups.

Each database has a specific maximum number of references that you can import into EndNote. Below is a summary of the most frequently used databases in biomedical and pharmaceutical sciences.

  • PubMed

< 200 records: Sent to > Citation Manager

≥ 200 records: Sent to > File > Medline (format) > creates .txt file.

in EndNote:  Import > select your .txt file > select NLM as import option

  • Embase≤ 10 000 records: Export > RIS format > select number of references
  • Google Scholar≤ 20 records: first add the required references to My library by activating the starOpen ‘My library (on the right under Sign in) and select the required referencesClick on Export > select EndNote
  • Web Of Science

≤ 500 records: click on Export to >  EndNote Desktop > Number of records (select)


≤ 200 records: Share > Add to folder: Results > Export

200 records:  Share > E-mail a link to download exported results > Option RIS format > send yourself an e-mail. Unzip the received file and save in (H-drive)

in EndNote: Import > select file > tick RIS as import option

  • Scopus

≤ 2000 records: Click on Export > select RIS format > Export

If necessary, import the created file into EndNote.

  • Select the references that you want to export > Export selected citation(s)
  • Select the format Plain Text > tick Include Abstract > Download and save

Comment: do not save as RIS file

  • In EndNote: click on Import > select the correct .txt file
  • Import option: Cochrane Library (Wiley) (select) > Import

TIP: It is preferable to import 1 record at a time. For that reason, make sure that you have only the required reference in your results before you export to EndNote. Otherwise you will have to export at least 10 of all the results found in a particular search query.

  • Select the specific study that you want to export > Download (top right)
  • Select the file format: Plain text > Download
  • In EndNote: click on Import and select your .txt file. Select the import option ClinicalTrials > Import

TIP 2:

In EndNote manually add the ‘Access Date’ in your reference (in EndNote). For some reference styles this information is even requested.

  • Menu References > New Reference
  • Reference Type: Web Page
  • Fill in the following fields: Author (person or organisation), Year, Title, Access Date, URL

TIP 1: For the web page of an organisation, add a comma at the end of the organisation’s name. Otherwise EndNote will interpret it as a person’s name. For example: World Health Organization (could be converted to ‘World, H.O.’)

TIP 2: if the publication date is unknown, enter ‘n.d.’ (no date) for Year. Under Access Date enter the date of the 1st consultation.

Comment: the appearance of a web page in a reference list depends largely on the Output style that you indicate in Word in the EndNote X9 tab.

You can transfer a database created in Reference Manager to a version in EndNote. Click here for the step-by-step guide.

In the same guide you will also find a step-by-step explanation of how to convert your Word documents linked to Reference Manager into a new link: between your Word document and your EndNote library.

Do you use the EndNote software through the Athena platform?

The software of EndNote has already been automatically converted in Athena to the newest version, X9.3.X. When you open your EndNote library/-ies, you will be asked to convert to the X9.3.X version.

You should get this notification:

For the safety of your data, be sure that before you click on ‘OK’, you make a manual back-up of your library/-ies.

Don’t hesitate to contact the KCGG in the case that you encounter troubles while opening your EndNote X9.3.X converted library.


Is your EndNote software installed locally on your desktop (only possible for UGent staff)?

We advise you to prepare your EndNote library/-ies for the conversion to X9.3.X. You have to prepare for conversion before you install the software update to EndNote X9.3.X! You can find a detailed step-by-step guide for on this link.

Manual EndNote

Manual Endnote X9

Courses EndNote X9

The KCGG offers short Blits information sessions as well as advanced workshops for EndNote. Click here to find an overview of the available courses.

Question for KCGG

Do you have a question related to your literature review or do you need help with searching, processing or publishing of your literature/data? Then please fill in our form to give us a clear view of your question and so that we can advise you efficiently. Alternatively, you could email us at kcgg@ugent.be.