EndNote

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. 

• Step by step process
• Backing up and maintaining your Library
• Removing duplicates from a large EndNote Library
• Screening references for relevance using EndNote - multiple reviewers
• Sharing your Endnote Library
• Exporting your Endnote Library to other screening software
• Creating a random sample set from your EndNote Library
• Using EndNote to update a search

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. Download a copy of the PRISMA Flow Diagram as an editable Word document.
3. Export records from your databases one by one and make a record of the number of records from each database for PRISMA reporting.
   • Optional step: If you anticipate a large number of records, and wish to follow the deduplication method described by Jane Falconer from the London School of Hygiene and Tropical Medicine, then you should export the records from your databases in the order specified by the method. 
   • Optional step: If you want to keep a record of which results came from each database, you can tag the EndNote records with the relevant database name as you import them. You should keep this EndNote library, which includes the tagged records, and copy all the references to a new EndNote library in which you can work with your search results, removing duplicates and screening the records.
4. Back up your EndNote library - you will need to do this at regular intervals during the process.
5. Remove duplicate records We recommend using EndNote for this as it allows absolute control over the process but note that some screening software options have automatic deduplication available within them. Once you have removed duplicates in EndNote, the duplicate references will all be in your EndNote library’s ‘Trash’ folder. Create a back-up of your library and make a record of the number of duplicate records for the PRISMA Flow Diagram. The records to use for screening will be in EndNote’s ‘All References’ folder.
   • Optional step: If you have a very large library, then we recommend that you follow the steps outlined by Jane Falconer from the London School of Hygiene and Tropical Medicine, which offers a time saving method to remove duplicates.
6. Screen by title and abstract in EndNote or specialist screening software to exclude any obviously irrelevant records. Create an EndNote Group to store your excluded references. If you are unsure, do not exclude the record, and carry it through to the full text screening stage. Record numbers of papers excluded for the PRISMA Flow Diagram. The records to carry forwards to the next step will be in EndNote’s ‘Unfiled’ folder.
   • Optional step: Multiple reviewers may wish to follow the process outlined by W.M. Bramer, et al.
7. Retrieve full-text documents EndNote's ‘Find Full Text’ function will help. UCL staff and students can also use UCL Explore to find full-text publications, and NHS staff can use the NHS Knowledge and Library Hub. Don't forget you can make use of our Interlending and Document Supply Service to access materials from other library services. Create an EndNote Group to file records of publications that you have not found as full-text publications. Record numbers of publications you have not been able to retrieve in the PRISMA Flow Diagram. The records to carry forwards to the next step will be in EndNote’s ‘Unfiled’ folder.
8. Screen the full-text documents applying your inclusion and exclusion criteria. Record exclusion reasons in EndNote (you can use groups to assist with this) or screening software.  Record also in the PRISMA flowchart. The records that remain in EndNote’s ‘Unfiled’ folder should be recorded in the final box in the PRISMA Flow Diagram.
9. Use the appropriate PRISMA Flow Diagram to record any publications found using other source in your PRISMA Flow Diagram. You may decide to add records for these publications to EndNote.
10. Use the included references in Word You will need to make sure that all the references you add to the Word document for your systematic review come from a single EndNote library.
    • Optional step: Import journal terms lists for your discipline if available. This can help to standardise journal names when you add them to Word. The journal terms list(s) should be added to your EndNote library before you add any references to it.
    • Optional step: Copy your included references to a new EndNote library. You can then add any other references you will be using in your review to this new EndNote library in order to use them with Word.
11. Updating your searches If it has been over 12 months between performing your searches and publishing your review then it is advisable to update your searches before your review is published. EndNote can help you to identify new records published since your original search.

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 consistent name so that you can easily identify the stage your library was at and the date it was last worked on e.g. "2024-04-29 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.

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. 

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. 

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. 

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. 

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.

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.   

For more information about how to record your search strategy, review protocol and methodology you can watch this video: Recording the details of your systematic review search.

This video is part of our online Systematic Reviews Searching Lesson. 

Contents

• 0.00      Overview.
• 2.31      Add database search results to EndNote.
• 6.07      Remove duplicate records from your EndNote Library.
• 10.56    Screen the de-duplicated records and exclude those that do not match the inclusion criteria for your review.
  • 12.17    Title and abstract screening in EndNote.
  • 15.55    Find the full text publications of any records that have not been excluded after title and abstract screening.
  • 20.20    Full text screening.
• 23.47    Prepare your EndNote Library so that you can use the included references in Word.

Links included in the video:

Options for obtaining full-text publications: