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Citing & Writing in the Health Sciences

EndNote Web, Endnote Desktop

Working with References - use the tabs below for different ways to get and work with references

Get References 5 Ways

1) Direct Export - send references directly from a database to EndNote.

*Each database/browser may have slightly different wording and steps.*

  • Select the references you need (in some databases save these to a Folder or List first).
  • Look for language like Send To, Export, Cite... (in some databases this is available from a Folder or List).
  • Choose Citation Manager, EndNote, or Direct Export in RIS Format and choose Open with EndNote.


2) Importing Text Files - a database creates a file. Save and import the file to Endnote

*Each database/browser may have slightly different wording or steps.*

  • Save database references as a text file.
  • Import into EndNote using the corresponding Import Filter.



3) Enter references manually - sometimes, you may have to add references by hand



4) Import PDF's

  • File > Import > File... or Folder...
  • Browse to your saved PDF of folder of PDFs using Import File: Choose...
  • Select PDF from the Import Option: dropdown menu and Import.

EndNote looks for a DOI in the first few pages to find the corresponding reference on In some cases your PDF may not have a DOI or it is not visible to EndNote (due to formatting or if it is an image PDF). In many cases it may be preferable to search for and export the reference from a database even if you already have a PDF copy.



5)  Create a Tab-Delimited Import

This abbreviated method works best with a simple list of DOIs and article titles. For full details and customization watch the Importing Tab-Delimited Files video below.

  • Identify the reference type by putting the text *Journal Article in the row above the data or table.
  • Make sure data or table headers use the appropriate EndNote field name. For example DOI and Title in this case.
  • In Excel Choose File > Save As > Save As Type: Text (Tab delimited) (*.txt)
  • Import into EndNote using the tab-delimited import filter.

EndNote can use a DOI to find reference updates and fill-in remaining fields. For this reason you may only want to create a tab-delimited file with a few key fields to save time. For details see the Find Reference Updates section of the EndNoteX8 Help file.

Need to bulk import large numbers of search results?

EndNote libraries can hold an unlimited number of records (exception: Sync library limit of 50000 or computer storage space).

However, databases may limit the number of records for specific export methods.

To get the maximum number of records out of CINAHL, MEDLINE, and PUBMED at one time use the steps below.

*Other databases may have different limits, wording, and steps.*

CINAHL - To export batches up to 25000:

  1. Select Share then Export Results: Email a link…
  2. Complete the e-mail form, choose RIS Format, and select Send.
  3. You will be e-mailed a link to a .zip file. Download and extract the file.
  4. Within EndNote select File > Import
  5. Browse to the saved file, choose Import Option: Reference Manager (RIS), and Import

MEDLINE - To export batches up to 1000:

  1. Select All or specify a range of results (e.g. 1-1000) in the Range window
  2. Choose EndNote from the Export To menu and select Complete Reference.
  3. Then, Export Citation(s).

PUBMED - To export ALL search results:

  1. Select Send To without marking any individual search results
  2. Select File, choose Format: MEDLINE, and select Create File.
  3. Select EndNote from the Open with menu if requested.

Get Organized

Use Groups to help keep your references organized.

Create groups manually or use Smart Groups and Combination Groups to automatically organize your references.

Watch the video or get details on Creating Smart and Combined groups from EndNote.

Find Duplicates

As you add to an EndNote Library routinely check for duplicates.

This can help prevent major headaches when using Cite While You Write with your writing.

Watch the video below for more details from EndNote.

How to Export References from EndNote into Excel

Step 1: Determine reference types.

  1. Scan your entire Endnote library noting all of the reference types included.  You can also sort your Endnote library by Reference Type so it is easier to scan all the reference types. Reference types include: generic, journal article, book, book section, conference proceeding, thesis, to name just a few.
    • This is very important because each one needs to be accounted for when developing the output style templates.

Step 2: Create an output style.

This step allows you to determine which fields, and in which order, you want to appear in your excel file.

  1. Select Edit, then Output Styles, then New Style.
  2. A new window should open.  Under “Bibliography” on the left-hand side select Templates.
    • This is where you add in what information that you want to be transferred over.
  3. Select Reference Types and select your reference type.  Eg. Journal Article.
    • You need to create a reference type for each reference type you included in your systematic review.  Eg. Journal articles, books, book section, generic, etc.
  4. Choose the fields that you want exported to you excel file.
    • To insert a field select Insert Field.
    • You can choose whatever fields you want to analyze in your excel file but we recommend these fields in this order:
      • Record Number → Reference Type → Name of Database → Author → Year → Title → Abstract 
      • The fields (Author, Year) that you should hide to prevent bias during the title/abstract screening are grouped together to make it easier to hide.
    • After you insert each field you need to insert a tab. Select Insert Field, then Tab.
      • Tabs show up as arrows.
      • Ensure that you insert a tab after your last field (abstract)
  5. Repeat steps 3 and 4 for every reference type in your EndNote library.  Make sure you select the same fields in the same order for all reference types, otherwise your columns in excel will not line up properly between reference types.
  6. Set author name preference.
    • This step ensures that your author names show up in a consistent format. 
    • Under “Bibliography” on the left-hand side select Author Name.
    • Beside “Initials”, from the drop-down menu choose full name.
    • Beside “First author” select Smith, Jane.
    • Beside “Other authors” select Doe, Jane.
  7. Select File, then Save As and give your output style a name.
    • Recommended Name: Excel Style or name of your systematic review
  8. Select Save and close the window.

Step 3: Remove carriage returns.

You need to remove carriage returns so that your data shows up cleanly in Excel.

  1. Select all your references to be exported.
  2. Select Edit, then Find and Replace.
  3. Beside In select Any Field from the drop down menu.
  4. Click in the “Find” text box.  Select Insert Special, then Carriage return.
  5. In the “Replace with” text box type “; ” (a semicolon without the quotations, and make sure to put a space beside the semi-colon).
  6. A window will pop up informing you how many references contained carriage returns, and asking you to confirm that you want to replace them.  Select OK.
  7. A window will pop up telling you how many changes were made.  Select OK.

Step 4: Export file from EndNote.

  1. Select All References on the left-hand side.
  2. Select a reference, right click, and select Select All or select one reference and select ctrl+A.
  3. Select File, then Export.
  4. Beside Output style, select the excel style that you created. You may need to search for it if you do not see your style in the drop down menu.
  5. You can change the file name if you wish, and choose a location.  Leave the Save as type as Text File.
  6. Select Save.

Step 5: Import file into Excel.

  1. Open Excel.
  2. Select File, then Open, then Browse.
  3. Beside the “File name” select Text Files from the drop-down menu. Find the file you exported from EndNote and select Open.
  4. A Text Import Wizard will open.
  5. Make sure that under “Original data type” “Delimited” is selected.  Select Next.
  6. Make sure that under “Delimiters” “Tab” is the only thing checked off. Select Next.
  7. Make sure that under “Column data format” “General” is selected. Select Finish.
  8. All of you records should have imported into Excel.  Scroll down to the last line and ensure that the line number is the same as the number of All References that you exported.
  9. You may need to adjust the columns to see your data clearly. You need to wrap text so that you can read the abstracts and titles
  10. Add column names (Record Number, Reference Type, etc) by inserting a new row at the very top of the Excel worksheet. You can freeze this row for ease when screening (under View, select Freeze Top Row).
  11. Save the file as an Excel Worksheet. File, Save As, choose Excel Workbook from drop down File Format menu (otherwise file will be saved as txt and all formatting will be erased).


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