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Systematic Searching Course

Session Three Recording

Welcome to Session Three!

We'll conclude the crash course by reviewing our translations, running our searches, and exporting our results into EndNote. 

Below you'll find steps to export your results from each of our crash course databases. If you have more questions on EndNote, the EndNote Research Guide is a great place to get started. 

Exporting Citations From PubMed

After you've ran your search:

  1. Click the “Send to” button (located in the top right above your results list).

  2. Select “Citation manager” from the dropdown menu.

  3. Choose how many citations to export. You can choose between all the results on the page, results you've hand selected, or all the results up to 10,000 citations.

  4. Click “Create file” — this downloads a file with a .nbib extension.

Exporting Citations From Scopus

After you've ran your search:

  1. Click the “Export” button at the top of the results list.

  2. When you press "Export" a pop-up menu will appear first listing file types and then listing different citation manager by name. You can select ".RIS" or "EndNote" from the latter list to get a file that will import to EndNote.

  3. In the Export Document Settings window:

    • You can download up to 5,000 citations without an account and up to 20,000 with an account. To download your entire search select the option that says "Documents 1 to" and then there will be a place for you to enter a number. When you make that selection you'll enter your total number of articles from your search in that box. It will remind you how many there are by saying "You can select up to X documents," provided you've done a thorough search and have less than 5,000 or 20,000 articles.

    • Under Output, choose the fields you want (e.g., citation information, abstract, keywords—recommended).

  4. Click Export to download a .ris file to your computer.

Exporting Citations from Embase

After you've ran your search:

  1. Press the square selection button to the left of where it says "results" at the top of your search

  2. Go the drop down menu beneath that button and select the option that includes your entire search results.

  3. Press "Export."

    1. You have to be signed in to export more than 500 records at a time but you can make a personal Embase account for free!

  4. In the export window:

    • Under Export format, choose RIS format (for EndNote, Reference Manager, ProCite).

    • Under Fields, select the information you want to include (e.g., citation, abstract, keywords—recommended).

  5. Click Export to download a .ris file to your computer.

Importing Your Searches Into EndNote

  1. Find the file in your downloads and go ahead and move it to a file that makes sense for your organizational scheme
  2. You can simply double click the .ris file to open it while EndNote is open.
    1. OR you can go to File at the top of the screen, scroll through the drop down menu to "Import" then find your file in the file explorer and select it.

Deduplicating Your Searches

Since you just did the same search in three different databases, there's bound to be some duplicates in there. This is where the deduplicate function can help get rid of those duplicate citations!

After you have all of your citations imported:

  1. At the top menu bar go to "Library"
  2. Select "Find Duplicates"
  3. A pop-up box will appear showing duplicate citations side-by-side so you can compare them and choose which one you want to keep and which one you want to get rid of.
  4. You can go through them manually in this way or you can select cancel and when you return to your Library all the duplicates will be selected for you to drag and drop them into the trash located in the menu on the left-hand side of the screen.

Organizing Your Citations

Groups (Manual Organization)

  • Groups are folders you create to manually sort references by topic, project, or paper.

  • To create one: right-click My Groups in the left panel and select Create Group.

  • You can drag references into groups, and the same reference can exist in multiple groups without duplication.

  • Perfect for simple organization or short-term projects.


Group Sets (Hierarchical Organization)

  • Group Sets are folders that hold multiple groups—ideal for big projects with many subtopics.

  • Right-click My Groups and choose Create Group Set.

  • Example: A Group Set called Capstone Project might include groups like Background, Methods, and Analysis.


Smart Groups (Automatic Organization)

  • Smart Groups automatically populate based on search criteria you define.

  • To create one: go to Groups > Create Smart Group, then enter your search terms.

  • Example: A Smart Group with the term "vaccine"[Title] will auto-collect any reference with vaccine in the title.

  • Great for ongoing research and keeping up with newly added references.


Star Ratings and Read/Unread Indicators

  • Use the star icon to rate the quality or priority of a source (1–5 stars).

  • The dot icon marks whether you’ve reviewed the reference (gray = unread, white = read).

  • These are useful for screening articles or marking stages of use.


Color Coding (New in EndNote 21+)

  • You can apply reference highlights (colored labels) to visually mark references in your library list.

  • This is especially helpful for quick-glance sorting, like “include,” “maybe,” “exclude,” or by topic area.

Using Cite While You Write

Cite While You Write (CWYW) is a feature in EndNote that allows you to insert and format citations directly within your Microsoft Word document as you write. It connects your Word document to your EndNote library, making it easy to add in-text citations and automatically generate a properly formatted bibliography in your chosen citation style.

When you downloaded EndNote you had to also close your microsoft products so that Cite While You Write could be installed into your version of word so, as long as you had Microsoft Word installed when you installed EndNote. When you open Word you should see an EndNote tab on your ribbon.

To use Cite While You Write:

Insert an In-Text Citation

  1. Place your cursor where you want the citation.

  2. Click Insert Citation > Find Citation on the EndNote tab.

  3. Search for a reference using keywords, author names, or titles.

  4. Select the correct reference and click Insert.

    • EndNote will automatically format the citation in your selected style and add it to your bibliography at the end of the document.

Choose a Citation Style

  1. In the EndNote tab, use the Style dropdown to choose your preferred format (e.g., APA 7th, Vancouver, AMA, JAMA).

  2. If your style isn’t listed, click Select Another Style to browse the full list.

  3. Your citations and bibliography will update instantly.

Edit a Citation or Bibliography

If there's a problem with a citation and you need to edit it, you need to find the citation in EndNote and edit the citation there. The changes will appear in your in-text and bibliographic citation.

The bibliography title is also auto-generated by EndNote so to change the text or formatting of the title you will have to go to "Configure Bibliography" in the EndNote tab on your ribbon to bring up a pop-up box to make those changes. 

Finding Full-Text

The Find Full Text feature in EndNote 2025 Desktop allows you to quickly locate and download full-text PDFs for references in your library without leaving the application. To do this:

  1. In EndNote, go to Edit > Preferences > Find Full Text.
  2. You may be asked for OpenURL link resolver or authentication credentials (e.g., for EZproxy).
    • OpenURL Path is:  https://resolver.ebsco.com/c/urqjfc/result?
    • Authenticate with: https://ezproxy.uthsc.edu/login?url=
    • Note that 1) the EndNote Find Full Text feature will not find everything for you. Some journals and database services (e.g., JSTOR, EBSCO, sciencedirect.com) will not work with it. 2) If your computer is on campus, you do not need to enter Authenticate with URL
  3. EndNote will begin finding Full-text for your articles in the background. It will automatically add a PDF to the citation's entry if it's available. These citations will have a paperclip to the side of them as an indication of the file. If it can find a authenticated URL but not a PDF that will be added to the citation but there won't be an indication on the file.
  4. The status of all of your citations can be found in the "Find Full Text" section of your menu to the left inside EndNote.

Thank You

I appreciate your efforts in this crash course. You'll maintain access to your spreadsheet, and I encourage you to download a copy and continue to practice storing your searches so you can use them again in future projects. If you have any questions or need more support in the future, please reach out!