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Guide to using EndNote reference management software

Using EndNote for Systematic Reviews

Before using EndNote for a systematic review we recommend ensuring that you are familar with its basic functions by either attending one of our scheduled training sessions, or by working through the self directed training activities. It is also important to be aware of how the various steps in a systematic review should be recorded and reported. 

If you are carrying out a systematic review or any literature review project where you need to take a systematic and transparent approach to conducting and reporting your search, this will require accurate documentation of all stages of your review process. EndNote is one piece of software which can support you with this. 

Typically, a systematic review will follow the PRISMA reporting standards and these include minimal reporting standards of the search and screening process to ensure transparency. EndNote can help you with the recording and reporting process for this by allowing you to store large numbers of references and providing methods for organising those references.  The following sections provide advice over EndNote's key functionality to support you with the process. You can also follow the step by step process below. 

Using EndNote for your systematic review: Step by step

Once you've finalised your database searches in your different databases you'll be ready to export the records into EndNote. 

  1. Create a new Endnote Library, saving it onto a local drive (not a network drive or cloud storage).
  2. Import journal terms lists for your discipline if available.
  3. Export records from your databases one by one. If you anticipate a large number of records and wish to follow the deduplication method described by Jane Falconer then you should export the records from your databases in the order specified by the method. 
  4. Back up your EndNote library - you will need to do this at regular intervals during the process.
  5. Create a group for each database and move the imported references from each database into them. 
  6. Add keywords to your references with the appropriate database name using the Name of Database field- this can be useful later on. Create a back up of your library and make a record of the number of records from each database for PRISMA reporting.
  7. Remove duplicate records. We recommend using EndNote for this as it allows absolute control over the process, but note that some screening software have automatic deduplication available within them. Create a back up of your library and make a record of the number of duplicate records for the PRISMA flowchart.
  8. Screen by title and abstract in EndNote or specialist screening software to exclude any obviously irrelevant records. If you are unsure, do not exclude the record, and carry it through to the full text screening stage.
  9. Retrieve full text documents. EndNote's Find full text function will help. Don't forget you can make use of our Interlending and document supply services to access materials from other library services. Record numbers for PRISMA.
  10. Screen the full text documents applying your inclusion and exclusion criteria. Record exclusion reasons in EndNote (you can use groups, custom fields or the research notes field to assist with this) or screening software.  Record also in the PRISMA flowchart. 
  11. Updating your searches. If it has been over 12 months between performing your searches and publishing your review then it is advisible to update your searches before your review is published. EndNote can help you to identify new records published since your original search.

Backing up and maintaining your library

We strongly recommend that you create compressed backups of your EndNote Library at various key stages during your systematic review, and you can do so following these instructions.

Create a folder for your library back up copies to be stored in and give your back up copies a consistant name so that you can easily identify the stage your library was at and the date it was last worked on e.g. "2021-04-29 Systematic Review Duplicates Removed". You will not typically need to access these back up libraries, but they act as a safety net in case you want to re-visit your search records from an earlier stage of your review (i.e. before duplicates were removed), or in case your working library is damaged/corrupted.

If you are frequently moving between different computers, synchronise your working library with EndNote Web. Note that you can only sync one EndNote Desktop library to any EndNote Web / EndNote Online Classic account, so only sync your main working library. If you attempt to sync a different library you will get an error message.

The main stages of the review where you should make compressed back up copies are:

  • After export from all databases and before duplicates are removed.
  • After all duplicates are removed.
  • Any other point after you have undertaken a substantial amount of work in your library, for example when you have screened many references.
  • Before attempting to do something major to your library e.g., find full text for a large number of references.
  • Some people may like to make a daily back up. If you are doing this you should overwrite previous daily back ups so that you do not end up with hundreds of back up libraries.

Tagging references with the name of a database

It can be useful to keep track of which database a record was originally downloaded from. Sometimes records include this within the Name of Database field, but this is very variable.

When you first import your references it is useful to create a Tag or Group for each database. You can also include these numbers in your PRISMA flowchart.

If using Groups, you may not want to maintain these original groups if you are screening using EndNote (many people screen from unfiled references), so to create a permanent record of where a record originated from you can use the Change/Move/Copy Fields Tool to add a keyword to your references with the name of the database they came from. 

  • Select the group of references which you wish to add a keyword with the database name. e.g. Medline.
  • Follow the instructions to perform a bulk edit of references to replace the Name of Database field. 

Removing duplicates from a large EndNote Library

EndNote has an inbuilt deduplication function that can be used to help you to identify and remove duplicates. You can edit the fields that EndNote checks to find duplicates in Preferences. Duplicates can be sent to the Trash or you can create a group for them. 

If you have a very large EndNote Library then we recommend that you follow the steps outlined in the link below by Jane Falconer from the London School of Hygiene and Tropical Medicine, which offers a time saving method to remove duplicates.

Don't forget to make a compressed back up of your EndNote Library before you start to remove duplicates and ensure you have a record of the total number of references before duplicates are removed for your PRISMA flowchart. 

Screening references for relevance using EndNote

You can use Groups to help you screen references within EndNote. Bramer, Milic and Mast have proposed detailed methods on how to do this, including how to compare EndNote libraries where there are multiple reviewers involved in the screening process. 

Sharing your Endnote Library

If you're working with other researchers on a review, you may need to share your EndNote library.

If you want to perform blind screening of references then library sharing will not be suitable as you can see the changes made by others. Blind screening can either take place in separate EndNote libraries or you can consider using screening software instead. 

Exporting your Endnote Library to other screening software

You may want to use a screening software for the screening stage of your review, especially if you are working in a team with multiple reviewers.Software can make screening with multiple reviewers more straightforward. 

You should de-duplicate your EndNote library first before exporting it - some screening software does have deduplication features but they are not considered to be as reliable as using EndNote's deduplication features.

You will need to save all the references from your EndNote library as a RIS file to export it. 

Creating a random sample set from your 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 Tools menu, then Output Styles and New Style. 
  2. In the new screen in the left hand panel, select Templates under the heading Bibliography.
  3. In the main panel of the same screen, 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, click on any reference in the central panel. In the right hand pane click on the summary tab for the reference. At the bottom of the screen use the dropdown showing the referencing style to pick 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 References. 

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.

Using EndNote to update a literature search

It is advisable to update literature searches before publication if it has been over 12 months since they were originally performed. This ensures the review will be based on the most recent evidence. Updates to published systematic reviews can also be performed to highlight any new evidence that has been published and make changes to recommendations where appropriate.

EndNote can be used to assist with the search update process and we would recommend that researchers follow the method developed by Bramer and Bain in 2017.