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Citing & Writing in the Health Sciences

An introduction to EndNote Desktop for Windows and EndNote Online / Web (free version).

Use the tabs below for different ways to collect and work with references

 

There are multiple methods for adding references to an Endnote library. References can be imported directly from a database search. Each database/browser may have slightly different wording and steps.

1) Import references directly from Pubmed, Medline and Cinahl. Video tutorial below.

  • Select the references you want to import. Look for language like Send To, Export, Cite, etc.
  • Choose Citation Manager, EndNote, or Direct Export in RIS Format and choose Open with EndNote.
  • Find information on how to set up direct export from databases on macOS

 

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

  • Save database references as a text file.
  • Import into EndNote using the corresponding Import Filter
  • Each database / browser may have slightly different file names or steps

 

3) Direct Export from Google Scholar to EndNote Desktop and EndNote Online

  • Go to Settings "three horizontal bars" in the upper left-hand corner.
  • Under Bibliography Manager, click on the drop down menu and select Refman, click Save
  • Search and select citation to add to EndNote library. Choose Import into Refman
  • Select Open with EndNote X9 if using Firefox or save and import using EndNote Import Filter
  • You can only import one reference at a time

 

4) Import stored PDF's

  • In Endnote go under File > Import > choose a pdf 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 crossref.org. 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.

 

Need to bulk import large number of search results? EndNote libraries can hold an unlimited number of records. However, databases may limit the number of records for specific export methods. 

To get the maximum number of records out of Pubmed, Medline and Cinahl at one time use the steps below.

____________________________________________________________________________________

PUBMED - To export ALL search results:

  1. Select Send To without marking any individual search results
  2. Select Citation Manager, choose All Results, and select Create File.
  3. Select EndNote from the Open with menu if requested.

___________________________________________________________________________________

MEDLINE - To export batches up to 1000:

  1. 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).

___________________________________________________________________________________

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

 

Use Groups to help keep your references organized. To automatically organize your reference get details on creating Smart and Combined Groups from EndNote. 

 

As you add to an EndNote library routinely check for duplicates. This can help prevent major headaches when you start writing your paper. 

  • Under the References menu, select Find Duplicates
  • Compare references on the side by side window and decide which version to keep
  • For each set of duplicates, you have the option to:
    • Click Keep This Record to save that particular reference and throw the other one in the Trash.
    • Click Skip to leave both references in the library, intact. They will appear in a temporary Duplicate References group, so you can review them later.
    • Click Cancel to automatically instruct EndNote to select the most recently-entered version(s) of each duplicate reference as the one(s) to be removed

Check videos on how to remove and track duplicates for systematic or scoping reviews with step-by-step instructions. 

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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