Part 1: Create a reference library

Welcome to this EndNote X9 guide by the Karolinska Institutet University Library. The main purpose is to provide course material for our workshops in EndNote X9.

The Endnote software allows you to collect, organize and maintain a library of references, find and save full-text journal articles, and insert and format references in a MS Word document. The references and PDF's in your library are searchable.

We strongly recommend that you always work with one library only. Using several Endnote libraries can in the long run create problems.

The Endnote library should be kept on your own computer. Don't store an Endnote library on any cloud service and do not store a working library on a flash drive. If you choose to use the Endnote sync feature you will save the library on the Endnote cloud service and have access to it via Endnote Online or the Endnote app.

Also, make sure to back up your library at a regular basis using the Compressed Library command (for libraries smaller than 5G) or the Save A Copy command for larger libraries.

Import references

There are four principal ways to import references to Endnote:

  1. Search for references in a specific database, select the references you want and then use the export feature in the database. In some cases you have to save the references in a file and import them.
  2. Connect to a database via the Endnote interface and import references directly.
  3. Import and create references from a PDF or folder of PDF's.
  4. Create a new reference manually.

Depending on your workflow and preferences, you may use different methods.

Option one is preferable if you are conducting a more advanced literature search. If you already know a selection of references to import, for example an author name or article title, you probably would benefit using option two. And if you have a collection of PDF's, option three would be most suitable.

Creating references manually is quite difficult and should be avoided. However, in case you do not find a reference in a database or library catalogue, for example a web page, creating a reference manually is necessary.

Import from Pubmed

  1. Conduct a search in Pubmed.
  2. Select references to import using the check boxes (or, for an individual reference, also the Cite button).
  3. Click on the Send to button.
  4. Choose Citation manager and click on Create File.

What happens next depends on your web browser:

  • Internet Explorer (PC) – the references will be imported to Endnote automatically.
  • Mozilla Firefox (PC and Mac), se below:

From the drop down meny (Open with) choose Other... and Endnote X9 (will be default after choosing a first time).

Any other browser (e.g. Chrome or Safari):

  • In Pubmed, choose File as destination and change the format to MEDLINE. Click on Create File. The file will be downloaded to your computer.
  • In Endnote, go to File and Import...
  • Select the downloaded file (with the extension .txt) and choose PubMed (NLM) in the Import Options list (this will be the default setting after choosing a first time).


Importing references from another database? See Part 4: More databases.​


Online Search – database searching via the Endnote interface

Using the Online Search functionality, i.e. connecting to a database via the Endnote interface, is convenient when searching for a specific article. For more advanced search functionality, use the database interface directly.

  • In this example we conduct an article search (author and title) in Pubmed. Be sure to change the search field.
  • The references will show up. Mark the references you want to copy to your library using the Copy References to command from the References menu or right click on the mouse, choose Copy References to and choose your library.

Import and create references from PDF's

You may import and create a reference from a PDF. Endnote uses the DOI (Digital Object Identifier) number in the PDF to extract bibliographic information from the article and create a reference. The program also attaches the PDF file to the reference.

Go to:

File → Import → File

If you want to import a folder of PDF's:

File → Import → Folder

If the PDF does not contain a DOI, Endnote will create a blank reference containing only the file name of the PDF file in the title field. The PDF will be attached to this blank reference.

If no bibliographic information is added, we suggest adding a DOI number in the corresponding field or a PMID (Pubmed ID) in the Accession Number field in the reference. Next, right click on the reference the select Find Reference Updates and the bibliographic information will be imported.

You can also use the PDF Auto Renaming Options, which automatically renames your PDF files to a more convenient name. And by using the& PDF Auto Import Folder, Endnote will automatically watch a folder on your computer for PDF's and import them. Go to → Edit → Preferences → PDF Handling.


Import PDF: manually

You can add files (up to 45 files for each reference) to the references in your library, for example full text articles in PDF.

  1. Start by saving an article in PDF on your computer.
  2. Mark the reference you want to add the PDF-file to.
  3. Go to References → File Attachments → Attach File or click on the paper clip in the reference.
  4. Find the file on your computer and click Open.

​You can also drag and drop the PDF file to a reference you already have in your Endnote library!

Import PDF: automatically

You can also locate and download articles in full text automatically.

This functionality works best with computers connected to the KI network (or another university network) as many of the articles in your reference library may be published in journals requiring subscriptions. If sitting outside the KI network, you only have access to free open access journals.

To make this functionality work smoothly, go to Edit → Preferences → Find Full Text and paste the following link in the field OpenURL Path:

  1. Select the references you wish to attach a PDF to.
  2. Use the magnifying glass with the pdf symbol in the tool bar or right click in the selected reference(s) and select Find Full Text.
  3. Endnote will start searching and downloading full text PDF's to the references.

In the column File Attachment you see which references have an attached file (article). You’ll find the result on the left panel of the Find Full Text operation.


Add a reference manually

If you don’t find your material in a database or library catalogue, or want to cite an unpublished document, the alternative is to add the reference manually. However this could be a bit tricky.

  1. Click on References → New Reference...

Fill in the appropriate fields. If you have another kind of Reference Type, for example Web Page or Social Media, select the correct type in the list.

View and annotate PDF

It's possible to make annotations and highlight text in the PDF's and to add sticky notes.

  1. Select a reference and click on the PDF tab.
  2. Use the toolbar to add sticky note or highlight text.

Take a closer look at the toolbar


Make an annotation in a reference

You can use the Research Note field to add a comment to a selected reference. Select the Reference tab to the left. You can make a note directly in the PDF file or you can write a comment in the Research Note field in the reference you have to the left side of the text.

Change the column headings

You have 10 columns, displaying fields from the reference, in your library. You can organize the display fields as you want.

Edit → Preferences → Display Fields (See figure below)

EndNote X9 – Preferences – Display Fields

  1. Choose Record Number in column 1.
  2. Choose Author in column 2.
  3. Choose Year in column 3.
  4. Choose Title in column 4.
  5. Choose File Attachments in column 5.
  6. Choose Research Notes in column 6.
  7. Make your own choices for the others.


Create groups

You may organize your references into groups. However, all the references are always stored in the All References folder. In the left panel there are different kinds of groups, either temporary or permanent.

If you delete a reference from All References you’ll find it in the group Trash (until you empty it). It gives you an option to take the deleted references back to your library. If you delete a reference from a group it stays in All References.

A new library begins with a single custom group set titled My Groups. However, you can create up to 500 custom group sets in your Endnote library.

  • Group sets can contain any combination of groups and smart groups. Name it as a heading of the groups.
  • Group To add a reference to a group you just drag and drop the reference to the selected group. Or right hand click on the selected reference and use the the option Add References To.
  • Smart Groups use search criteria to dynamically update groups as existing references are edited or new references are added to the library.
  1. Click on Groups
  2. Create a Group, a Group set or a Smart Group.





You can easily drag and drop a reference(s) into a specific Group. You can add the same reference in many Groups. You can also organize the groups into group sets by dragging and dropping the group to a named Group Set.

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