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Stony Brook University

Systematic Reviews: Running the Protocol

A guide to conducting systematic reviews.

Running the Protocol

  1. Once the protocol is set and agreed upon, run it through at one time, recording the date it was done.
  2. Collect and de-duplicate all of the results from the search protocol. It's strongly recommended to use a software program such as EndNote to for collection and de-duplications. See Citation Management for more information.
    1. Mark abstracts with source database
    2. Record how many abstracts collected per search & per database
    3. Delete duplicates (record final number of abstracts post-deduplication, in total and per database)
  3. Screening can be done in EndNote, but it is easier to use a program such as Covidence to allow reviewers to read the abstracts and, later, full text, and record inclusion/exclusion decisions. The transfer of the deduplicated set of abstracts to Covidence is not difficult; export from EndNote as an XML file and then import into Covidence.

Citation Management

It is extremely valuable to collect the results of all the searches into a citation management software.This will help with tracking, de-duplicating, and screening.

At Stony Brook, we provide access to the EndNote Program via DoIT's SoftWeb. The Health Sciences Library has a Guide to Using Endnote.

Additionally, the online version of EndNote is available through a free registration via the Web of Science database. Register in WoS and then use that same login email and password at

Other citation management programs are available online or for purchase.

The Stony Brook Libraries provide regular workshops on how to use EndNote; alternatively, you can contact a librarian to request training and assistance. See Health Science Librarians or Melville Library Library Liaisons to find the librarian who works with your specialty area.

A useful video on how to use EndNote for Systematic Reviews is available from R. Wright, Johns Hopkins Medical Institutions.


EndNote has an automated "Find Duplicates" function that will help locate many of the duplicates, but be careful! It isn't always accurate and it never gets all of the duplicates. Unfortunately, deduplicating for a systematic review almost invariably requires someone to go through by eye. Sort the articles in EndNote by either Author or Title and look for the duplicates - checking the volume, issue and page numbers are often the fastest confirmation. Track the number of duplicates you remove by database and in total. This can be done pretty easily in EndNote. See a librarian for assistance if needed.