Referencing guide at the University of Manchester: EndNote for Systematic reviews

It is always worth creating a back-up of your library prior to you making any lasting changes such as the de-duplication and screening processes. 

1. In the EndNote toolbar select File > Save a copy
2. Alternatively you can create a compressed library version (for email or copying purposes) by selecting File > Compressed Library (.enlx).

You may wish to name your file after the stage of the review process you had reached e.g.

February 2024 Before Duplicates Removed

Different databases often have overlapping coverage, increasing the chance of duplicate findings.  

It's important to exclude these duplicates from your final tallies for accurate reporting, sparing the need to review and screen the same document multiple times. 

EndNote will search the currently selected references for duplicates.

1. To search the whole EndNote Library, click on the All References folder. 

2. In the Endnote toolbar select Library - Find Duplicates. 

2. Compare duplicate references to decide which to keep. The display automatically highlights any differences it has detected between the references, if any. You can copy and paste information between references if necessary. 

3. If you select Keep this record the other record will be sent to Trash. 

4. If you want to keep both records, or decide later, click on Skip to go to the next duplicate. 

5. If you decide to Skip or Cancel, references are held in a temporary Duplicate References group. The Duplicate References group is discarded when you close your library.

6. Duplicate references are highlighted. You can delete all the duplicate references by dragging and dropping into the Trash or right click on any highlighted duplicate, and select Move references to trash.
   

To catch any outstanding duplicates, it can be helpful to manually look through your library. 

• Make sure to organise your centre pane where your references are displayed so that you can see all the useful fields clearly to help you judge whether a reference is a true duplicate. 

• Right click in the column headers in the central pane to add or remove any columns in the display.

1. Setting your output style to Annotated.

• It can also be useful to set your output style to Annotated so that the reference preview includes the abstract. 

• To change your outpout style - In the EndNote toolbar select Tools - Output Styles - select Annotated.

2. Sort your references by the Title field.

• In the central pane click on Title in the column header.
• You can then look through to check for duplicate titles. Be aware that sometimes different publications can have the same title.   

3. Sort your references by DOI.

• Right click in the column headers in the central pane and select DOI to add it as a column.
• You can check where references are organised by DOI, although not all records will have a DOI (and in some cases the DOI might be the same for different references, e.g. conference abstracts).

4. Sort your references by page number.

• Right click in the column headers in the central pane and select Pages to add it as a column.
• Checking by page number can also be helpful finding duplicates.

You can check or change the criteria for deduplication:

1. In the EndNote toolbar select Edit > Preferences and select Duplicates from the box menu to see the criteria. 

Organising references into groups lets you:

• Keep results from individual databases together in one set.

• Create ‘group sets’.

• Create smart groups which update as you add to your library.

To create a group or group set: 

1. In the EndNote toolbar select Groups. Alternatively you can right click on any of the groups / group sets in the left pane, e.g. My Groups and select Create Group Set or Create Group. 

2. Name your Group/ Group set. 

3. To move a reference into a group:

   • Click and drag references from the central panel into a group.

   • Use the Ctrl key to select more than one or Ctrl+A or for Mac Cmd+A to select all references then right click and select Add References To> and you will see your list of groups. 

If you remove a reference from a group, it will remain in your library and can be found in All References. You can put a reference in more than one Group, which will not duplicate the reference. 

To see which Group a reference is in click on the reference to highlight it, select References in the EndNote toolbar, and select ‘Reference Summary’. 

Temporary groups

Some temporary Groups are automatically created when you carry out certain functions in EndNote: 

1. Duplicate References: This Group shows the results when you search for duplicates in your library. 

2. Imported References: This Group shows the last set of references imported into the library and is replaced each time you import a new set of references. 

You can open Groups in new tabs to easily move between them.

1. Select a group, right-click and Open in new tab. 

A smart group is dynamically populated with references that fulfill your specified search criteria as you add references to and edit references in the library. 

1. In the EndNote toolbar select Groups - Create Smart Group.

2. Give your smart group a name and fill in the criteria you want for the group by using the drop down menu to select an appropriate field or fields, e.g. fill in an author name in the Author field to add all papers by a specific author to that group.  

3. You can also pick the Keywords field from in the dropdown menu if you want to add keywords to create a Smart Group that includes all references that have that particular keyword. 

4. You can add your own labels to your references by entering them in the ‘keywords’ field in the right-hand side edit screen. You can then create smart groups of all references with particular keywords. 

Groups can be shared with other EndNote users if you are also using EndNote Online Classic. You will also be able to see any Groups which have been shared with you by others. See sharing a library for more information. 

To share a library
1.    Select File > Share.
2.    Add the email of those you want to share your library with. You need to specify whether they have Read & Write access or Read Only.
 

Specialist tools like Covidence and Rayyan are great when you are screening results as part of a research team. Reference management tools are also perfectly adequate when screening results on your own. 

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 an RIS file to export it.  

Screening your results in EndNote 

1. Following the same process as above create a Group Set and name it as Screening, within the group set create three groups named: Accept, Maybe, Reject.

2. Select the All References folder and move the record into the appropriate folder based on your inclusion/exclusion criteria. You may find having a Maybe folder useful as you find yourself getting into a flow: a mindset where you are clear on your criteria and can see from the title and/or abstract whether a paper will be accepted or rejected. Anything you are unsure about gets put in the Maybe folder which you come back to later. 

3. You might want to organise your rejected papers by the reasons for their rejection, based on your inclusion/exclusion criteria. You could create folders for this in a similar way — e.g., Reject: qualitative; Reject: review paper, etc. You will only do this if you intend or are required to report on the reasons for rejecting papers. Do note that the screening will take longer. You can now report on the final number of papers included in your systematic review. 

Your groups should look something like this: 

Figure 3: group structure for screening in EndNote 20 

This article by Bramer, Milc and Mast takes you through the process step by step, including how to compare Endnote libraries when working with colleagues.  

• Reviewing retrieved references for inclusion in systematic reviews using EndNote 

Bramer, W. M., Milic, J. & Mast, F. (2017). ‘Reviewing retrieved references for inclusion in systematic reviews using EndNote’ J Med Libr Assoc, 105 (1), pp. 84-87  https://doi.org/10.5195/jmla.2017.111.

When you import references of journal articles from databases, they arrive with either the abbreviated or full journal name as part of the reference, depending on how that database stores references. 

This poses a potential problem if you import a reference that contained the full journal name, but want to write for a journal that requires an abbreviated name in the referencing style. 

You can solve this issue by updating your journal term lists: 

Open an EndNote library, then navigate/click as follows:

1. Library 

2. Define term lists [a dialog box will now appear. In the box, navigate/click as follows…] 

3. Lists (tab) 

4. Highlight ‘journals’ (central pane) 

5. Import list [a dialogue box will now appear. Browse the .txt files for an the appropriate term list] 

6. Double click on a file (it should automatically import into your library) 

7. Click OK 

8. Finished! 

You can import more than one term list file if your research is cross discipline (repeat the step above).