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Systematic Reviews, Scoping Reviews, and other Knowledge Syntheses

Exporting search results to EndNote

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 to search for an updated or additional filter.

Exporting from Ovid Online

(MEDLINE, Embase, APA PsycInfo, Global Health)

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):

  1. In EndNote, create a new library, with a useful name like SearchConcepts-MEDLINE-yyyymmdd-xRecords.enl, for the records from the database in question (e.g., MEDLINE on Ovid) and have the library ready in the background
  2. From Ovid, export complete reference in groups of <= 6,000 at McGill (e.g., 1-2000, 2001-3000; be careful if exporting in batches of 6,000 as Ovid may time out), do this until all of your records are exported (Export > Export To: EndNote; Select Fields to Display: Complete Reference; Export Citations)

  1. Move batches of exported records to the library you created and check the final number of records in the library against the number of results listed in database
  2. Document the search: From Ovid MEDLINE, use the command and copy/paste the search into another document, or download the search history for your records using Export (select one record for this) > choose Microsoft Word format, check off Search History, and save the Word document to your documentation folder, with a useful filename in a format like SearchConcepts-yyyymmdd-Search-MEDLINE-xRecords, SearchConcepts-yyyymmdd-Search-Embase-xRecords, etc. You can delete the record from the Word document as that was only needed to permit exporting the search history.
    • The search history can then be copied and pasted into an appendix of the article, to document the search strategy with exactness. Avoids transcription errors
  3. Save the search history to your personal Ovid account (free) and identify the search by database name and date; this greatly facilitates rerunning the search later if an update is needed. Document your Ovid account information as well.
  4. Create a compressed version of the EndNote library for your records

Exporting from PubMed

  1. In EndNote, create a new library, with a useful name like SearchConcepts-PubMed-yyyymmdd-xRecords.enl, for the records from the database in question (PubMed) and have the library open in the background
  2. From PubMed, Click on Send To > Citation manager > Selection: All results > Create file

Click "Send to" button and select "citation manager" from options

Change the "Selection" to "all results"

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:

In Firefox, select "Open with" and make sure EndNote is the application selected

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)

To import a file into EndNote, choose the file saved on your device, e.g., pubmed_result.txt, use the Import Option PubMed (NLM), and click Import


  1. Document the search: Save the search history for your records by clicking Create alert under the search box once you are viewing the results or from the Advanced screen, click Download (upper right corner of History and Search Details) to maintain the line-by-line version (if applicable). The search in Create alert is saved in an agglomerated format but this is useful if you need to rerun the search later for an update and is also valid when including the search strategy in your manuscript
  2. Create a compressed version of the EndNote library for your records

Exporting from Web of Science

  1. In EndNote, create a new library, with a useful name like SearchConcepts-WoS-yyyymmdd-xRecords.enl, for the records from the database in question (Web of Science) and have the library ready in the background
  2. In Web of Science, Click on the arrow for the Save to EndNote online dropdown menu and select Save to EndNote desktop
  3. Export full records in groups of up to 1000 (e.g., 1-1000, 1001-1243)
  4. Move batches of exported records to the library you created and check the final number of records in the library against the number of results listed in database
  5. Document the search (copy the query link as well)
  6. Document which parts of Web of Science Core Collection you are searching (Web of Science Core Collection is composed of multiple databases and access to them is insititution-dependent)
  7. Create a compressed version of the EndNote library for your records

Exporting from CINAHL

  1. In EndNote, create a new library, with a useful name like SearchConcepts-CINAHL-yyyymmdd-xRecords.enl, for the records from the database in question (CINAHL) and have the library ready in the background
  2. In CINAHL, click on View Results for the list of records you will be exporting
  3. For large sets of records: In upper right corner, select Share > Export results: E-mail a link to download exported results (this option is activated at the institutional level, e.g., it's available at McGill but may not be available at other institutions) 
  4. Enter the email address to which to send the records and make sure RIS Format is selected in the right-hand column
  5. You will receive an email (sometimes the delay can be a few hours, and you have 36 hours for the download) with a link to a .zip file: Save the .zip file to your computer and then extract the file
  6. From EndNote, Go to File > Import > File, choose the extracted file, and make sure the Import Option is Reference Manager (RIS) (If it's not an option, click on Other Filters... to find it)
  7. Document the search

Exporting records from Google Scholar

You can use a tool called Publish or Perish (download the program)

Note: You Cannot have syntax errors in your query or you will get 0 results

Export up to 1000 records > Save file as RIS (the EndNote option does not seem to always work)

If using EndNote, you may be able to update the bibliographic information up to a point: Select all (or do in smaller batches given the process can take a lot of time), go to Menu: References > Find Reference Updates

  • Will automatically replace missing data and add updated/corrected data if needed
  • Can take time
  • The abstract may still not be available: When it comes time to remove duplicates across multiple databases, import these records last in the deduplication process (e.g., into EndNote if you deduplicate in EndNote, or into Covidence if you use their deduplication feature), so that better quality records (i.e., those imported before the Google Scholar records) are prioritized


Creating a backup, compressed EndNote library for your records

  • Before merging the libraries, create compressed libraries of each of the EndNote libraries from the individual database searches: Keep these compressed libraries for your records (you can also back these up as, e.g., RIS files, to save space)

Creating a new EndNote library for deduplication and backup after deduplicating

Using the uncompressed versions of the libraries containing the exported records (if you saved the records in multiple libraries), bring all the records from your separate searches in to one EndNote library if you haven’t done so already: From EndNote menu, File > Import > File > locate individual .enl files; Import: EndNote library. You will perform deduplication in this library. Import the records of higher quality first, and the lesser quality records last (e.g., first from PubMed/MEDLINE on Ovid, last from Google Scholar)

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.

EndNote workshop handout

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Due to a large influx of requests, there may be an extended wait time for librarian support on knowledge syntheses.


Find a librarian in your subject area to help you with your knowledge synthesis project.


Or contact the librarians at the
Schulich Library of Physical Sciences, Life Sciences, and Engineering

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