Note: This procedure helps you keep track of the information that will be needed to report the methods in the article and also to fill in the PRISMA flow diagram.
Have the right EndNote library open in the background before you begin exporting.
Note: We do not generally recommend using Safari as your browser during this process, although it can be used with some tweaking.
For more instructions on using EndNote or other software programs, please see the Citation Guide
The steps below cover Ovid MEDLINE, Embase Classic+Embase on Ovid, PubMed, Web of Science databases, and CINAHL on EBSCO.
If EndNote does not seem to include an export filter for the database you are using (for example, ICTRP) or the available export filter does not seem to be working properly, search the web for [database name] EndNote export filter, or visit https://www.endnote.com/downloads/filters/ to search for an updated or additional filter.
We often start by exporting records from Ovid MEDLINE, if applicable (you may have decided to only use PubMed to search MEDLINE; those instructions are below):
Depending on the browser you are using and/or your computer setup, this will: (1) export the records directly to EndNote, or (2) prompt you to choose to use EndNote to open the file, or (3) save it as a .txt file which you would then need to import into your library.
Choose to use EndNote to open the file:
Import the .txt. file:
If the file was saved to your computer instead of automatically being imported into EndNote, import the file into EndNote (In EndNote menu: File > Import > File and locate the saved PubMed file on your computer) > Select PubMed (NLM) filter (if not visible, click “Other Filters…” to find it)
See the instructions on deduplicating in EndNote.
Create a compressed library for backup after having removed all duplicates, with a filename like SearchTerms-yyyymmdd-Deduplicated—xRecords.enlx. This will be the library for screening.
Systematic review software may offer this functionality, or you can use one of the following methods to remove duplicates from a merged EndNote library.
Before deduplicating, you will need a merged EndNote library containing the records from all your separate EndNote libraries for the individual database searches, if you had previously exported records from each database into separate libraries:
Using this merged library of records from your individual database searches, you are now ready to remove duplicates. Here are two methods you can use:
1) Earlier version of "Bramer method" for deduplicating, with steps provided in Word document format:
2) Paper describing more advanced configuration options for removing duplicates in EndNote: Bramer WM, Giustini D, de Jonge GB, Holland L, Bekhuis T. De-duplication of database search results for systematic reviews in EndNote. Journal of the Medical Library Association : JMLA. 2016;104(3):240-243. doi:10.3163/1536-5050.104.3.014
Create a compressed library for backup after having removed as many duplicates as possible, with a filename like SearchTerms-yyyymmdd-Deduplicated—xRecords.enlx. This will be the library for screening. You can export the deduplicated library to Rayyan, for example, or other synthesis software, to facilitate the screening process, which usually involves more than one reviewer.
Use the online Deduplicator tool. This is a new version as of August 2021.
The offline DeDuplicator (old version) may be useful for large sets of records (which used to be considered ≥ 2000). Download the SRA-dedupe-UI application from GitHub. As of October 2020, there were only Linux and Windows versions available.
Keep a copy of the RIS or XML file for your records.
See also: Rathbone, J., Carter, M., Hoffmann, T., & Glasziou, P. (2015). Better Duplicate Detection for Systematic Reviewers: Evaluation of Systematic Review Assistant-Deduplication Module. Systematic Reviews, 4(1), 6. doi:10.1186/2046-4053-4-6