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EndNote X9

Guide to using EndNote reference management software

FAQs / troubleshooting

Accessing EndNote and EndNote versions

Viewing and displaying references and libraries

Adding references

Sharing references and libraries

Editing references and libraries

Using EndNote with EndNote Online

Technical problems

Using EndNote for systematic reviews

I already have a free (basic) EndNote Online library. Will this change when I join UCL?

When you start at UCL you will be able to access EndNote Desktop from a UCL computer. You will then be able to sync your existing basic EndNote Online library which will activate the full version of EndNote Online, regardless of the email address you have used to register your EndNote account.

What will happen to my EndNote Online library once I leave UCL?

Once you leave UCL, you will retain the full version of EndNote Online for 12 months after you last synchronised it with EndNote Desktop, after which it will revert to EndNote Basic. You will not lose any references.

Can I download EndNote to my own computer?

Is it possible to transfer a Windows EndNote library to EndNote on a Macintosh (and vice-versa)?

Libraries that are created on the Mac or PC version of EndNote are compatible across platforms. You can transfer the files via portable media or you can email them to yourself.


In Endnote X9 compatible with earlier versions of EndNote?

With the new features and database structure of EndNote 8 and later your libraries will not be backwardly compatible with older versions of EndNote. See this page for information on how to convert libraries created in an earlier version of EndNote.

EndNote X9.3 introduced a new database engine to EndNote. EndNote X9.3 and later libraries will not be backwardly compatible with older versions of EndNote. See this page for information about EndNote X9.3 and EndNote 20: Library Conversion and Backward Compatibility.

Can I change which fields are displayed in the database view?

  • Go to the Edit menu and select Preferences and Display fields
  • From here you can choose which field to display in up to eight columns. Change the heading by typing in the heading box. Note that this doesn’t change the names of the fields, only the headings of the columns.
  • Then click OK
  • Alternatively, right click anywhere on the field columns header to select and deselect fields to display.

My references have not imported correctly

This will depend on accuracy of the information in the source where you got your reference from, and the accuracy of the import filter. Import filters often operate without you realising, if you are exporting references directly from an online database. 

Sometimes data fields will be populated incorrectly or missing. First, check that the data was actually in the source itself - for example, often journal articles will not have a volume or issue number if they are published electronically ahead of print.

You can also try exporting from the source in a different file format, if the option is available. Often a .RIS file works well, in some cases BibTex. Refer to Exporting from Online Resources for advice on specific databases.

If I delete references from a group within EndNote will they be removed from the main library itself?

If you use the Remove References from Group command (found from the Groups menu, or right-click) the reference(s) will only be removed from the group. If you select Move references to trash the reference(s) will be deleted from the main library itself.

How many references and full text or file attachments can a library hold?

EndNote X9 Desktop can hold an unlimited number of references and file attachments.

Can I use Adobe Acrobat to view, highlight and annotate linked PDFs in my library?

In EndNote X9:

  • Click on the PDF preview tab from the right hand panel.
  • Right click and choose the program to open the PDF with.

Note: Sticky note comments inserted using the default EndNote reader are searchable by choosing 'Any Field and PDF' or the 'PDF Notes' search options. They are not searchable when inserted using another program.

Remember PDFs are saved by default to the PDF section of the library’s accompanying .Data folder. 

Can I export my references to Excel?

Please refer to documentation from Clarivate on exporting references from EndNote to Excel.

When I try to export references from an online database, why does it open Zotero instead of EndNote?

How can I get my existing Word list of references into EndNote?

There are several possible solutions to this. Note that these techniques will get the references into EndNote, not the full text of the item.

Use Google Scholar or UCL Explore

  • Sign into your GS or Explore account.
  • Search for each item on your list individually. When you find the item add it to My Library (GS) by clicking on the start icon, or My Favouries (Explore) by clicking on the pin icon.
  • When you have added all the references, go to My Library (GS) or Saved Items (Explore). From these spaces you can download in bulk all of your saved references to EndNote. See Exporting from Online Resources.

Use HubMed Citation Finder

This technique will only be useful if the majority of your references can be found in PubMed.

  1. Go to HubMed Citation Finder.
  2. Copy and paste your references, ensuring that each different reference is on a new line.
  3. Click Search.
  4. Review the matches and select the right one for each reference. Selected references are highlighted yellow.
  5. Download all selected citations by clicking the Download all selected citations button at the bottom of the screen. The references will be downloaded in the citation format specified (RIS or BibTex).

If I search a database from within EndNote, will I get the same results as if I searched the database itself?

We would not recommend carrying out a comprehensive search using the tools from within EndNote. Searching ths database itself will give you a far richer range of options for constructing a search and managing the results.

Searching from within EndNote can be very useful if you know the details of a particular reference you want to find, or if you only want to carry out a very quick search for a few references.

Can I transfer references from other reference management programmes into EndNote?

You can transfer references from other reference management programmes into EndNote:

Please also see support from Clarviate on the following topics:

Can I transfer all the references in my Mendeley library to EndNote?

It is possible to move references from one reference management programme to another. You may also move any PDF attachments. To transfer references from Mendeley to EndNote:

Exporting the references from Mendeley Desktop

  • Select the references you would like to move. Hold down the Ctrl key to select more than one.
  • Go to the File menu and select Export.
  • Change the Save As Type option to EndNote XML. By default the exported files will be named 'My Collection'.
  • Ensure you make a note of where you are saving the file and click Save.

This will export a .Data file and a .xml file.

Importing the references into EndNote

  • Go to the File menu and select Import File.
  • Click Choose and browse to the .xml file which was exported from Mendeley ('My Collection.xml').
  • Change the Import option to EndNote generated XML.
  • Click Import.
  • Go to the File menu and select Exit.

Importing the PDFs into EndNote

Recall that every EndNote library is made up of a .enl file and a .Data folder. You will need to know where these files are located on your computer.

  • Navigate to the 'My Collection.Data' folder which was exported from Mendeley.
  • Open the 'My Collection.Data' folder . If there is a PDF folder inside, copy it.
  • Navigate to the .Data folder which is associated with your EndNote library.
  • Paste the PDF folder into the EndNote .Data folder.

You should now find that the pdf files have been attached to the references in your EndNote library.

Can I share my EndNote library with a colleague?

Can I email an EndNote Library to a colleague?

Yes, but you must use the compressed file format to save your EndNote library first, and then email this version of the library. The compressed file format will save a copy of your library as a single file. Go to the File menu and select Compressed library. The library will be saved as a .enxl file.

See also Sharing a library.

What is a travelling library?

Each formatted citation in your Word document is saved with field codes that embed reference information in the document. This comprises a "travelling library" of cited references which means anyone who has EndNote installed on their desktop can work on the document, even if the EndNote library file is not present.

The bibliography can be recreated from the travelling library although some fields such as abstract and notes are not included.

This means that if you had a Word document with some formatted EndNote citations, but did not have access to the original EndNote library which was used to insert them, you can still use the references and work on the document. The reference information can be extracted from the Word document and used to populate a new (or existing) EndNote Library.

  • In Word, in the EndNote tab, click on Export to EndNote and then Export Traveling library.
  • You will be prompted to choose to Create a new library or Export to an existing Library.

Note that this feature does not work when citations are unformatted.

Can I make changes to many references at once?

To perform a bulk edit of references:

  • First ensure you have a list of references displayed for which you wish to make changes. The operation will be applied to all displayed references, not all highlighted references. You can always create a Group in order to display the relevant references together. 
  • From the Tools menu, select Change/Move/Copy fields.
  • Select the appropriate field and type in the text you wish to copy to that field for all references in your list. You can choose to have the text appear before or after any existing text in the field, or to replace it.

Warning! If you are appending additional content to existing text in a field, the additional text cannot then be removed as a group edit.

I have de-duplicated my library but I still have some duplicates

The duplicate search works by comparing information in some selected fields. Differences in formatting of journal names, author names and page numbers can mean that duplicate items are not picked up by the duplicate search. Where there are slight differences in these fields the duplicates will not be detected.

You can amend the de-duplication criteria to attempt to detect additional duplicate references. To improve the search to find such items switch off one of these parameters at a time before re-running duplicate search.

Can I find and replace data in multiple references at once?

It is possible to do this but be cautious about making changes to references which might affect your citations or bibliography.

  • First select the references that you want to edit.
  • Click on Edit and then Find and replace.
  • From the In drop down list, select the field to be searched.
  • In the Find box, type the text to be changed and in the replace box, the text to replace it.

How can I use custom fields?

EndNote has eight custom fields which you can use for your own purposes. To be able to see the custom field and add information to it, you must first name that field in the template for the relevant reference types:

  • From the Edit menu, select Preferences and then Reference Types.
  • Click on Modify Reference Types.
  • Next to the relevant Custom Field, enter a name for the field.
  • Click on Apply to all Ref Types to ensure the field is available in all reference types. Then click OK.

How can I merge two EndNote libraries?

Please see advice from Clarivate on merging EndNote libraries.

Why won't my library sync?

  • You can only sync one EndNote desktop library to any EndNote Online account. If you attempt to sync a different library you will get an error message.
  • Check the details in the Sync settings in EndNote desktop:
    • Go to the Edit menu, select Preferences, and Sync.
    • Try resetting the EndNote Online password details. This may need doing if you have reset your EndNote Online password, e.g. because it was forgotten. 
    • Check that the correct file path for your library is showing in the Sync this EndNote Library box. If you have moved your EndNote library it will not be able to sync.

How can I download EndNote to my own computer?

My EndNote library says that it has been corrupted, and I can't open it. Is there anything I can do?

Try the database recovery tool by going to the Tools menu, then Recover library. This may help to repair a damaged library, but doesn't always work. To avoid data loss remember to back up your library regularly.

See also The proper process for recovering library files.

Why are references that I export from online sources automatically imported into Zotero (or another reference management package) instead of EndNote?

Where there is more than one reference management package installed on a computer, which is the case with Desktop@UCL, there can be conflicts between the packages. Where references are automatically imported into the incorrect package, you may need to change your default application.

My library is now marked "read-only". How do I disable this feature?

Multiple users can access one EndNote library simultaneously on a network drive as long as the library is restricted to read-only or locked status. This will allow the user to perform searches, copy information to their documents and format their papers but not make any changes.

To switch off read-only, simply right click the unopened library/file and select Properties and then ensure the "read-only" box is unchecked.

Warning! EndNote libraries on shared network drives or cloud storage are easily corrupted. You are advised to backup your library regularly.

I've accidently deleted my library! Is there any way of retrieving it?

Yes! But only if you still have the saved .Data folder. When EndNote opens a library, it first checks the contents of the .Data folder, and only uses the information in the .enl library file if the .Data information is missing or corrupt. So, using the .Data folder you can essentially trick the program into restoring the original library.

Simply create a plain text file, and rename the file using the original library name, followed by the .enl file extension. Your original restored library will now open as normal.

See also The proper process for recovering library files.

How can I select a random sample of records from an EndNote Library?

If you and others are screening your results to determine which ones to use to inform your research study, you might wish to test your screening procedures by getting all researchers involved to screen a random set of 10-20 references to compare results before screening the entire set. Follow these instructions to ensure a truly random selection from your EndNote library.

Create an output filter that exports EndNote record numbers 

  1. Open your EndNote Library and go to the Edit menu, then Output Styles and New Style. 
  2. In the new screen, select Templates under the heading Bibliography. 
  3. Put your cursor in the box below Generic. Then, click Insert Field and select Record Number
  4. Go to the File menu, select Save As and save it as something descriptive like record-number-only

Use the output style to export the record numbers for all the records in your EndNote Library

  1. In your EndNote library, use the dropdown menu towards the top left of the screen, to Select Another Style… and search for your previously created Output Style. 
  2. Then select the Choose button and ensure that your output style name is displaying in the dropdown box. 
  3. Select EndNote’s All References folder to make sure all your references (that you want to create a subset from) are displayed. Then select one of the references in the middle pane and press ctrl + a (or cmd + a on a Mac) to select all references. 
  4. Right-click on the highlighted references and select Copy Formatted

Randomise the numbers using Excel 

  1. Open Excel, and press ctrl + v (or cmd + v on a Mac) to paste all your record numbers into a blank worksheet. 
  2. In the cell to the right of your first record number, insert the formula =rand(). This will create a random number from 0 to 100. 
  3. Hover the cursor over the bottom-right corner of the cell until it makes a cross. Then click and drag all the way down to the last row that contains a record number.
  4. Insert a row at the top and select Sort & Filter and then Filter from the menu bar. 
  5. Then, sort the second row (with the random numbers) from smallest to largest (or largest to smallest). 
  6. You now have a randomly sorted list. Select and copy the top x number of cells in the first column (however large you want your sample to be). 

Use Excel’s CONCATENATE function to format the numbers so that the associated references can be retrieved 

  1. Open a new Excel spreadsheet. 
  2. Paste the column of numbers (your sample) into column B of the new spreadsheet. 
  3. In cell A1, type {# 
  4. In cell C1, type } 
  5. Hover the cursor over the bottom-right corner of cell A1 until it makes a cross. Then click and drag all the way down to the last row that contains a record number in column B. 
  6. Repeat step 5 for cell C1. 
  7. Put your cursor into cell D1. 
  8. Enter the following into Excel’s formatting bar: =CONCATENATE(A1,B1,C1)  
  9. This will create a number in D1 which will be in the format {#1234} 
  10. Hover the cursor over the bottom-right corner of cell D1 until it makes a cross. Then click and drag all the way down to the last row that contains a record number in column B. 
  11. Copy the formatted numbers from column D and paste into a Word document as text (not as a table). 
  12. Follow the instructions from step 4 on the EndNote How To Community Forum.