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EndNote: Endnote for Systematic Reviews

Endnote for Systematic Reviews

This guide will help you set up an Endnote library to export and screen results for your Systematic Review and to populate PRISMA flow diagram


When working on a systematic review, you should be searching multiple databases. Create an EN Group for each database you’ve searched, e.g. Medline, Embase, Scopus etc. Group sets can be used to group together the stages of the Systematic Review process, such as Searching and Screening. In the Screening Group set you can great Groups such as On-topic, Off-topic, etc. Groups will help you keep track of how many references were retrieved from each database and how many were (de)selected at each stage of screening process. You will use these numbers to complete the PRISMA flow diagram.

Group Sets

  • Create Group sets to organise your groups into sets.
  • From the toolbar select Groups > Group Sets
  • Enter the name of the Group Sets
  • You can add sub groups under Group Sets using the instructions for Create Group
  • The left pane of the Library window lists all of the Groups in the current Library

Custom Groups

  • Use Custom Groups to group references together (it may be for an assignment, a topic etc)
  • From the toolbar select Groups and click on Create Group
  • Enter a name for the Group

OR

  • Click on My Group and right click on the mouse, select Create group then enter a name of the Group.
  • Click on All References at the top of the Groups pane to view all references in your Library.
  • Highlight references you wish to add to the Group in the main window.
  • From the Groups menu at the top of the page, select Add References to… and choose your   
  • Group name from the list.     

OR

  • Highlight references you wish to add to the Group in the main window.
  • Drag and Drop to the right group


When working on a systematic review, you will need to export large numbers of search results from each database you search and move them to the relevant Group. Each database has different direct export options and different export limits. Refer to the Systematic Review toolkit Screening section for more information.

  • We recommend the Chrome or Firefox Internet browser for browsing our databases and transferring records to EndNote.
  • Most databases will have an option to “export to…” or “save references to…” button that will enable you to save to EndNote.
  • There is a list of major databases and brief instructions on exporting references to EndNote from them under collect references – Export from different databases.

Example: Direct export from ProQuest databases (eg.ProQuest Central, ProQuest Science Journals, ProQuest Research Library)

  • Leave your EndNote Library open.
  • Open your Internet browser and go to the Library homepage: https://Library.sydney.edu.au/.
  • Click on Databases.
  • Click on P under Browse databases A-Z by Title.
  • Scroll down the list of databases until you find the ProQuest databases.
  • Click on the database you wish to search.
  • Search the database on your topic of interest.
  • Select citations from the first page of hits to add to your EndNote Library.
  • Click on the Save link.
  • In the Export/Save drop-down menu select RIS (works with EndNote, Citavi, etc.).
  • Under Select Fields to Display select the Citation, abstract, indexing and Click on Continue.
  • The file may export direct to EndNote or may appear in the bottom left of screen above the Start menu. Click on the file ProQuestDocument…ris to trigger the direct export.
  • The records will appear in your EndNote Library.


When working on a systematic review, you might need to track a reference back to the database that it came from. To be able to do this, you will need to add database details to all the references imported from each database. This is an optional step, but we recommend completing it in case you need this information in the future.

Change/Move/Copy fields functions will help to add additional information to exported records, such as database name and the date and time that you have exported the search results.

Please note:

You should update database name field imediately after exporting a set of references to EndNote. To do this, select all references under Recently Added and follow the steps below.

Importance of checking everything before using the mass update because it can’t be undone. e.g. if you accidently choose ‘keywords’ instead of another field you might wipe over important  data

  • Highlight the references. Click on Tools > Change/move/copy fields…
  • Select Name of database from the list and type the information you like to add to the record.
  • Select Replace whole field with and click OK.


Documenting your search strategy and search results is important for the Systematic Review methodology section of your paper, and for completing the PRISMA flow diagram. It is very important to complete this step before proceeding to the next step (De-duplication).

  • Database names with the platform
  • Export Date
  • Search terms used in each database
  • Number of results from each databases
  • Grey literature sources searched
  • Other search techniques - hand searching, scanning bibliographies of pertinent authors, contacting experts
  • Limitations
  • Duplicates


Save a copy of your EN library before proceeding with this step. Go to File>Compressed Library and follow the prompts. Save the compressed file somewhere other than your working computer (e.g., on a USB drive, in the cloud storage). This backup will help if an accident happens.

When searching multiple databases, you will inevitably retrieve duplicate results. If you are planning to use Covidence or another screening software, it might perform deduplication and this step will not be required. Reserve the Trash folder for duplicates only. Don’t empty the Trash as duplicate results need to be documented in the PRISMA flow diagram.

If you are planning to use Covidence for screening, this step is not required.  Covidence will perform its own deduplication.

Once you have exported all your search results into Endnote, you will need to identify and delete any duplicate record(s). EndNote can automatically eliminate duplicate references if it includes the same author/s, year of publication and title as another record within the Library.

  • The Find Duplicates window highlights fields that contain non-matching text so you can quickly compare the records.
  • Select References > Find Duplicates
  • The Find Duplicates window will appear 
  • Compare each set of duplicate references.
  • Select Keep This Record to keep one of the duplicate references or select Skip to keep both references.
  • On completion of finding duplicates, go to the Trash under My Library in the left pane.
  • Right click to empty trash and remove the duplicate references from your Library.

It may be necessary to also look for duplicates manually as the EndNote find duplicate function may miss some duplicates references due to foreign characters or spelling variation.


When working on a systematic review, you will need to screen results by applying eligibility criteria. The first screening involves a quick scan of titles and abstracts to identify on- and off-topic articles. This screening can be performed by one reviewer only. Second screening involves applying the eligibility criteria and needs to involve at least 2 reviewers performing screening independently. Discuss with your second reviewer their preferred way of doing the screening. You might choose to:

  • create a copy of the EN library each and merge the copies later (Step 7)
  • use an online Sync option (Step 7)
  • export into Excel and work on separate sheets (Step 10)
In each case your will need to keep the process blind: each reviewer completes screening independently, then compare results and reconcile differences. Document your thoughts on the selection process to help with completing the PRISMA flow diagram.

You can using “Change/Move/Copy fields” function and research note fields to add your comments OR you can create custom records to add specific information about the record

Creating customised fields

  • Go to Edit>Preferences > Reference Type from the left hand side.
  • Click on Modify References type
  • Select the reference type and scroll down to Custom fields and type the name you wish to display on the display fields.
  • Click on Apply to all reference types and then click OK.

Adjusting EndNote library window to display customised fields

  • Go to Edit>Preferences> display fields from the left-hand side.
  • Select the custom fields as per your requirement and type the display name under heading.
  • Click on Apply and then OK.

Display fields name will be appeared on the library window


When working on a systematic review, you will need to involve at least one more person to screen and appraise the results. You will need to share your EN library with your second reviewer without revealing the results of your own screening process. Share your library with them before making your comments on the selection process.

Option 1: Compressed and attach as an email

  • File > Compressed Library (.enlx)
  • Select Create and With File Attachments then click on Next.
  • Select the destination you wish to save your compressed library.
  • Add the file name with date 
  • Click on save then EndNote will automatically compressed your library and data folder as a one file. 
  • You can attached compressed library to your e-mail to share with others.

Option 2: Share your EndNote library

You can find detailed instructions for Sync and sharing your library from the EndNote for Collaboration page.


When you have selected articles for full text screening and appraisal, you can attach full text PDFs to the relevant records. If the University of Sydney Library does not provide a full text option for the article(s) in question, please place a Resource Sharing request (one article per request).

When exporting references from databases or Library Search  into your EndNote Library, the data that appears in your EndNote Library is bibliographic information about your selected references only. Exporting references will not automatically export the full-text papers/articles. The Find Full Text feature is used to search across Library collections and locate the full text papers corresponding with references in your Library. It will automatically attach either the full text PDF files or URL links to full text papers to your references in EndNote. This feature will find many, but not all full text items for your reference list.

  • In the main Library window, highlight the references that you wish to locate full text for (click on Ctrl and A to highlight all, or alternatively select individual papers by holding down the Ctrl key and selecting references with your cursor).
  • From the toolbar select References > Find Full Text > Find Full Text.
  • Alternatively click on the Find Full Text Icon
  • Login to eResources using your UniKey and password or Library borrower number and name and select the Accept button shown on screen.
  • After logging in, click Continue.
  • Check the Copyright notice (see the Copyright page for assistance) and click Continue to proceed
  • EndNote will search for full text for the selected references.
  • A temporary Find Full Text Group will appear on the left pane. It will remain visible during the current session, but will disappear when you close the Library.
  • If EndNote is able to locate the full text, it will be attached to your reference, and you will see a paper clip icon next to the reference in the attachments column.
  • Note: Full text may not be automatically retrieved. This can occur due to your subject area, network speed, firewalls etc. If full text is not attached you can manually attach the full text using the steps below:

Attach Full Text Manually

  • Ensure that you have downloaded the full text file onto your computer or USB
  • In your EndNote Library, select the reference to which you would like to attach the PDF document
  • Click on the “Paper Clip” icon on the Quick Edit Pane  OR From the main toolbar select References >  File Attachments >  Attach File
  • Browse to locate the PDF file you saved previously onto your hard drive or USB
  • Select the required file and click on Open
  • The file will appear in the File Attachments field of the reference.


The PDF Viewer panel allows you to open, preview and annotate your attached PDF files in your EndNote library. This will help with data selection and appraisal for your systematic review. For more information, refer to Systematic Review toolkit Data extraction and appraisal section.

The PDF Viewer panel allows you to open, preview and annotate your attached PDF files in your EndNote library.

To add notes to a PDF

  • Go to PDF article tab
  • Click on the sticky note tool then click and drag over some text in the PD
  • Double click on the sticky note bubble that appears and type in your comment
  • Click the save icon to save your comments.

Highlight tool

  • Click on highlighting tool
  • Select the text that you want to highlight in the PDF. Selected text will highlight in yellow.
  • Click the save icon to save your highlights.

Search Sticky notes

  • Search the text of individual PDF files and/or their Sticky Notes using the search box
  • Select PDF notes (to search Sticky Notes) or PDF (to search PDF text) from the fields drop-down men
  • Type in the text you wish to find and click on Search


Once you have selected the final references for your systematic review you can export them to Excel where you can create graphs, tables, etc. You can also use Excel to share with your second reviewer and proceed with the screening (Step 7).

Export Endnote library to Excel

  • In Endnote select Tab Delimited style. In the style manager select another style> Tab delimited
  • Go to Edit>Output Styles>Edit Tab Delimited
  • In the edit menu go to bibliography>Templates
  • Click on insert field and add the following fields Author, Year, Title, Journal, Volume, Issue, Reviewer1, Reviewer2, and Reviewer3. Each field must be followed by the tab. (Please select the tab from insert field option.  At the end of the string add paragraph character.
  • Repeat above step for each referencing type you wish to exporting to Excel.
  • Go to file>save as and give a name.
  • Go to style manager>select the created style>select the references you wish to export. 
  • Go to edit and click on copy formatted.
  • Open Excel workbook and go to edit and paste (ctrl+V) the references. You may require to format the excel workbook as per your requirement.

You will need to create a new template for each type of references that you wish to export to Excel.