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Guide to Endnote X


Printable Word version

How do I?

 NOTE: Several versions of Endnote are loaded on computers at PML, MBA and SAHFOS, it is important to be aware that although Endnote version 7 libraries will be converted to later versions. libraries created in versions 8, 9 & 10 will not convert to version 7. Libraries created in Endnote 8 & 9 will work in version 10. If you are sharing an Endnote library you should check that you are all using the same version of the software.

Install Endnote on your computer

  •          Be careful when ITG install it from the network as all the functions may not work when logged on as yourself. To check, open Word and see if there is an Endnote option in the tools menu. Make sure you uninstall all earlier versions of Endnote and backup your libraries.

Create a new database

  • Choose new from the file menu and give the database and name and file location. Endnote will not work unless there is a database open.

Add references manually

  • From the references menu choose new. Choose appropriate reference type from the drop-down menu near the top of the screen.
  • Authors can be added in the format Woodason, E.M.
  • Journal titles should be entered in full.
  • There is no need to add punctuation at the end of fields, as the journal format will do this automatically.

Import references – 1) LIBWEB

If your references do not import correctly, replace the Endnote import filter with the filter available from the NMBL webpages.To replace the existing EndNote Import filter, click here to download the filter, unzip the filter and paste it into "C:\Program Files\EndNote X\Filters" when the software is loaded.

         Search for your references in LIBWEB and select the references you need by ticking the box next to them. Click on Download.  

         Choose the option "EndNote format"

         Click on Download and save the file as a text file to your hard disk.

         Open Endnote and the database you wish to import references into.

         Choose Import from the File menu.

         Click on the "Choose file" button and select the file that you saved in LIBWEB, make sure that "files of type" is set to All Files

         Import Option should be set to "EndNote Import"

         Click on OK and your references should be imported, to see the whole database choose "show all" from the "Reference" menu.

Import references – 2) WoS

  • To import references from WoS, log on to WoK and search for your references, mark them and go to your marked list.
  • If you only need the bibliographic information in Endnote, simply click on the Export to reference software button.
  • If you need additional information e.g., abstracts, keywords, author address, select these options from the table before clicking on the Export to reference software button.
  • Endnote should open with the box Select a reference library, find the file of your Endnote database, click Open and the references should be imported.

Import references – 3)ASFA

Downloading references from ASFA. If you do not select the full record format, your references will require substantial editing once they are imported into EndNote.

         To download references, search and select the records that you require and then click on the Save/Print/E-mail records button.

         Select the full record format (this is the only ASFA format containing the tags which allow records to import correctly)

         Next to the Save button, set File format to PC.

         Click on the Save button. In the browser window that appears select File, Save As and insert a file name. Save as type must be set to Text File (*.txt). Click on the Save button.

         Open your Endnote database and select File, Import. Choose your file from ASFA and set Import option to ASFA (CSA). Click on the Import button and your references should appear.

Import references – 4) Science Direct

  • Search for references
  • Click on export citations on results page.
  • Select all documents or marked record numbers
  • Select citation or citation and abstract from dropdown menu.
  • Leave default file format for Endnote
  • Click Export.
  • Endnote will open. Select the Endnote Library that you want to import the records to.
  • When you have opened the Endnote library, the records will import automatically.

Import references – 5) MOFR (NISC)

  • Select an output format on results page.
  • Click on Export
  • In the new window click on Endnote .
  • Endnote will open
  • Select the Endnote library into which you want to import records and the records will import automatically.
  • NOTE: Owing to the format of records in the MOFR database all records import as "generic" format and therefore require editing.


Import references - 6) Blackwell Synergy STM

If your references do not import correctly, replace the Endnote import filter with the filter available from the NMBL webpages.To replace the existing EndNote Import filter, click here to download the filter, unzip the filter and paste it into "C:\Program Files\EndNote X\Filters" when the software is loaded.

         Search for references

         Mark the records to export

         Click download all highlighted abstracts to citiation manager at the top of the results list.

         The list of references is displayed. Scroll down to foot of page and select the download options, Endnote is the default. Leave the box next to direct import highlighted.

         Click open when asked if you want to open or save the file.

         Endnote should open, select your library and the references should import.


         Duplicates can be discarded when importing references. In the Duplicates option of the Import box, choose either Import all, Discard duplicates, or Import into duplicates library. I would recommend that if you wish to remove duplicates on import that you import into duplicates library as Endnote does not always correctly identify duplicates and it may delete distinct references.

         To check your database for duplicates from the References menu choose Find duplicates. Duplicate references will then be shown with alternate ones highlighted, right click on a highlighted reference and choose Delete to remove your duplicate references.

         Selecting Preferences from the Edit menu can alter the criteria by which Endnote selects duplicate references. Click on Duplicates and choose the fields that Endnote compares when searching for duplicates, either an Exact match or Ignore spacing and punctuation can be chosen.

         To double check for duplicates, choose sort from the references menu and then sort by author, year, title, journal. Sorting in this way should make it easier to identify duplicates by eye.

Journal format/preview

         First ensure that Endnote’s toolbars are visible (they are not displayed on installation) by clicking Edit, Show toolbar and ensuring both the main and text style toolbar are displayed.

         To see how your references will be displayed in the current format choose References, Show Preview and selected reference will be displayed in a window at the bottom of the screen.

         To change the journal format a drop down menu should be visible with the list of journal formats that are available (to see them all choose select another style). Select the format you require.

Edit journal/output format

         If the journal format you require is not available from the list it is possible to edit, or even create completely new journal formats. It is easiest to select a journal format that is similar to what you need and then select File, Output styles and then Edit “whatever the current journal format is”. Here changes can be made to any aspect of the journal format including anonymous works, page numbers, journal names (full/abbreviated), citations, bibliography and footnotes.

         It is necessary to be an administrator on the PC to change these files as they are within the Programs folder.


Find/replace, add keywords

         To globally change text in the database (similar to find/replace in Word) select References, Change text and enter what you want to search for and to replace it with. It is sometimes easier to copy a selection from your database to ensure what you search for is accurate.

         To globally add something to your database, such as a keyword, select References, Change field. Select which field you want to change from the drop-down menu and select whether you want to insert at the start or end of field, replace the whole field with or clear the field. If you want entries such as keywords on separate lines you can add line breaks by pressing control and return at the same time.


         To search for references in your database, choose search from the References menu. You can then enter search terms and select which fields you wish to search (if in doubt choose Any field). If you wish to search for more than the default two terms that are shown, click on the Add button. You can combine search terms using the operators and, or, or not by clicking on the radio buttons. Click on the Perform search button and the references matching your criteria will be shown. Further searches on this subset can then be done, to return to the entire database select Show all from the References menu.


         Reference lists can be sorted by simply clicking on the name of the field you wish to sort by (e.g. Author, Year, Title buttons just beneath toolbars), clicking twice will sort them in the opposite direction.

         To sort by more than one field, say by Author, then date, choose Sort library from the References menu and choose the fields and whether you would like them sorted ascending or descending.


         If you select Preferences from the Edit menu, it is possible to change the setting for various parameters including: Libraries, Display fonts, Reference types, Temporary citations, Sorting, Change case, Formatting, Display fields, Duplicates, Online, Folder locations, Term lists and Spell check.


Show/Hide buttons

        Click the double triangle icon to toggle between Hide Empty Fields and Show Empty Fields. Initially, EndNote displays all fields in a reference. Click Hide Empty Fields to view only those fields that contain data. This setting is remembered until you click the icon again.

          By Clicking the double triangle icon at the foot of the screen you can display/hide a window which displays a reference in the journal format style of your choice.


         References can be exported as either a Text file, Rich Text Format or HTML. Choose Export from the File menu, assign a file name and file type.

Terms lists

         To edit a terms list select Open list from the Terms menu and then choose Authors, Journals or Keywords.

         The author list contains all the authors in the database and can be useful to spot anomalies in names.

         The journals list contains all the journals in the database and also options for entering up to 3 sets of abbreviations. Always enter the journal title in full and use the terms list to enter abbreviations.

         The keywords list contains all keywords in the database.

         If a terms list does not contain all the entries that you would expect it to, open a new database and import the old one into it.

Interaction with Word

         One of the most useful features of Endnote for scientists is the ability to interact with Word and to automatically create bibliographies.

         From within the MS Word program there should be an Endnote option in the Tools menu. Here there are various options including to find citations in your Endnote database, insert citations and to format the bibliography.

         See below for information on inserting charts, tables and figures into Word from Endnote.

         From your Endnote database you can select references (for multiple references hold down the Control key) and then go to Word and choose Insert selected citations from the Endnote menu.

         An Endnote bibliography in Word can be formatted with a different journal format by selecting Format bibliography from the Endnote menu. Only journal formats (output styles) that have already been used in Endnote will be displayed.

         To produce a complete bibliography in word, i.e. transfer your EndNote Library, select all the references in the EndNote library which you want to copy. Then either right click and select copy formatted OR edit, copy formatted, open Word and paste.


Saving/Copying your Endnote 10 Library


You can either copy the Endnote file and the corresponding .DATA file to another drive or you can save a compressed copy of the library. If you move your library to a different computer, or if you want to share your library with someone, remember to always copy the .DATA folder along with the library.

 Saving a compressed copy of the library

You can save your complete library (the filename.enl file as well as its associated .DATA folder and all of its contents) to a single compressed filename.enlx file in order to easily back up your library or send a copy to a colleague. Later, you can easily restore (unzip) the compressed library with EndNote.

To save to a compressed library file:

  • Open the library in EndNote.
  • From the File menu, select Send to and then Compressed Library.
  • Use the file dialog to save to an EndNote Compressed Library (filename.enlx).

To restore a compressed library file:

  • Use EndNote (version X or later) to open the filename.enlx file, which will extract the .ENL file and the .DATA folder to the same folder where the .ENLX file is located.
  • Use EndNote to open the filename.enl file as you normally would to use the library.


Linking to documents and web pages using Endnote 10

To link a file to any field in an EndNote reference:

  • Open the reference.
  • Type or paste, into any text field, the path and filename you wish to link. For example:


EndNote will display the full path to the file. The path and filename become hyperlinked— blue, underlined text—which you can click to open the file. Note that spaces in local folder and file names are indicated with “%20.”

Electronic Resource Number

An Electronic Resource Number is a unique ID for locating a digital version of a document, PDF, or image. It is most useful if you are importing reference data or retrieving references directly from an online source.

Use this field to insert the Digital Object Identifier (DOI) of a paper published in an e-journal, e.g. 10.1007/s01022-002-0216-y. DOIs in references import into this field in Endnote X, to create an active link to the paper using a DOI add the prefix http://dx.doi.org/doi: to the DOI number, e.g. added to DOI number 10.1046/j.1365-2419.1997.00036.x the link looks like this http://dx.doi.org/doi:10.1046/j.1365-2419.1997.00036.x

URL (Internet address) and linking to local files

A URL (Uniform Resource Locator) is the term for the address used to locate a specific page of information with your Web browser.

To link a URL to a reference in your EndNote library:

  • Select a reference in the Library window and open the reference. Put your cursor in the URL field.
  • Type or paste a valid URL into the field. For example: http://www.mba.ac.uk/nmbl or ftp://ftp.csa.com
  • The URL becomes a hyperlink (blue and underlined).
  • You could also link to a local file on your computer. Go to the References menu and use the Link to URL command to locate and link to a file, such as: file:///C:/Program%20Files/EndNote%209/Examples/Paleo.doc
  • Enter multiple URLs or file locations on separate lines.
  • Adding any other information along with the URL may keep the Open URL command from successfully finding the site.
  • When a correctly formatted URL is entered into the URL field, the Open URL command in the References menu can be used to launch your Web browser and take you to that site or file.
  • Web of Science and Science Direct include a URL for the full text of an article online. When importing or retrieving references directly from these sources, the URLs import directly into this field to take advantage of the Open URL command. You can also store a URL to related information on the Web or other relevant material.
  • Clicking on one of these links will open your Web browser and go to the address given. This feature is not specific to the URL field.


Linking to PDF:

  • Select a reference in the Library window, or open the reference.
  • From the References menu, choose PDF>Link To PDF.
  • On the file dialog, select a file to link to the selected (or open) reference.
  • Note the check box along the bottom titled, "Copy this file to the default PDF folder and create a relative link." This gives you the option to:
  • Select the check box to copy the original PDF file and place the copy in the DATA\PDF folder that is part of your EndNote library.
  • Deselect the check box to always have EndNote look in the original folder for the inserted file.
  • For more information about this option, see, “Selecting a Relative Path or an Absolute Path for Link to PDF” below
  • Click Open.

EndNote will display an icon indicating the type of file inserted. You can insert approximately 45 files into the same Link to PDF field.

NOTE: Another way to link a PDF file to the Link to PDF field is to drag and drop the file onto the reference in either the Library window or the Reference window. Whether the file is saved with the database or is linked with an absolute path is determined by the default PDF setting.

Selecting a Relative Path or an Absolute Path for Link to PDF

When you link a file to the Link to PDF field in a reference, you have the option of saving a relative path to the file, or an absolute path to the file.

What is a Relative Path versus an Absolute Path?

When you insert a link to a file with the PDF>Link to PDF command from the References menu, the file dialog includes a check box titled, "Copy this file to the default PDF folder and create a relative link."

Relative Path (check box selected)

When the check box is selected, EndNote makes a copy of the original PDF file and places it in the DATA\PDF folder that is part of your EndNote library. This saves the file as a “portable link” that can move as part of the library. EndNote will always be able to access the file, even when you share your library with a colleague (always include the complete DATA folder along with the .ENL file). However, if you change the original file on your computer, those changes will not be reflected in EndNote. You would need to clear the PDF file from your EndNote reference and reinsert the PDF file.

Absolute Path (check box blank)

When the check box is blank, EndNote will use the complete path and filename to look in the original folder for the inserted file. This can be helpful if you plan to edit the original PDF file, and you want those changes reflected when you access the PDF file from within EndNote. However, if you ever move the file from the original folder, EndNote will not be able to access it unless you clear the PDF file from your EndNote reference and reinsert it from the new folder location. If you send your library to a colleague, the PDF file will not be available.

Using the Open URL and Open PDF commands

The URL>Open URL (CTRL+G) and PDF>Open PDF commands on the References menu can be used to launch a URL or open a linked file entered into an EndNote reference under the following conditions:

1. When just one reference is selected in the Library window, the Open URL command opens the first URL that is listed in that reference’s URL field. The Open PDF command opens the first linked file that is listed in that reference’s Link to PDF field.

2. When multiple references are selected, EndNote checks the URL or Link to PDF field in each of the selected references (in the order listed), and opens the first link it finds.

3. If you need to enter multiple links into the URL field of one reference, enter them one per line. EndNote will open the first link in the field when you choose Open URL or Open PDF. If you have multiple links, you can click on any one of them to activate the link.

To open a linked file or Internet site from the URL field:

You could open the reference and click on the hyperlink found in the URL field. Or,

1. Select or open a reference in the Library window.

2. From the References menu, choose URL>Open URL (CTRL+G).

The Open URL command opens the linked URL with your default browser, or opens the linked file with the appropriate program.

To open a linked file from the Link to PDF field:

You could open the reference and click on the file icon found in the Link to PDF field. Or,
1. Select or open a reference in the Library window.
2. From the References menu, choose PDF>Open PDF.
The Open PDF command opens the linked file with the appropriate program. If the file was linked with a relative path, EndNote looks in the library's DATA\PDF folder to find the file. If the file was linked with an absolute path, EndNote looks for the file in the original folder from which it was inserted. 

Inserting Images and Captions

  • The Image field can contain a graphic or an object (file attachment). The Image field is included by default for all reference types. NOTE: Each reference can contain only one graphic or file attachment.
  • The image itself is copied to the [library name].DATA folder found in the same folder as the library file. If you copy Endnote libraries containing images, you must also copy the .DATA file.
  • A related Caption field appears directly under the Image field in a reference. Use this field for a short description of the image. The caption will be inserted with the image into a Word document. Use the Chart or Table reference type if you want to include an image and later insert that image as a table in Microsoft Word. Images in all other reference types will insert into Word as figures, which are listed and numbered separately from tables.

To insert a graphic (picture) into the Image field:

  • With the reference open for editing, go to the References menu and choose Insert Picture. (The Insert Picture command is also available on the toolbar.)
  • In the file dialog, locate the graphic file and Insert it.
  • EndNote recognizes at least these graphic file types: BMP; GIF; JPEG; PNG; TIFF
  • Valid picture files are those that Microsoft Word recognizes as pictures.
  • The graphic appears as a thumbnail within the reference. Double-clicking on the thumbnail will launch an associated application to open the graphic file, with the same effect as if you had double clicked the file on your computer desktop.

To insert an object file, into the Image field:

  • With the reference open for editing, go to the References menu and choose Insert Object. (The Insert Object command is also available on the toolbar.)
  • Click Choose File to display a file dialog.
  • Locate the file and Insert it. EndNote recognizes at least these formats:
  • The file will appear as an attachment, with the program icon and filename. (If the application used to create the document is not available on your system, the icon simply gives generic Windows file information.)

Opening the Image File

  • Double-clicking on a graphic or attachment icon in the Image field of a reference will launch an associated application (determined by the file type and your operating system) and open the file for viewing or editing.

To insert an image into a Word document:

  • Select Tools, Endnote, find figures
  • Enter the name of the image in the search box and click search
  • Select the image you want and click on insert.
  • The image and caption will be inserted into your document.
  • The list of figures does not automatically update if you delete a figure in the document. If you have moved or deleted image citations:
  • Select Tools, Endnote 9, Generate Figures List
  • This will regenerate the list of figures and associated citations.