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EndNote X9 Basic course

3.3 Direct export from a database into EndNote

What is "direct export"?
In some databases it is possible to export the search results directly into EndNote via a command in the databases. Via the command EndNote is started and you can choose a library in which you want to place the results.
This works fine in many databases (a.o. Web of Science, PubMed, Embase, PsycINFO). If this is the case, it is the easiest way to transfer references from a database to EndNote. If this feature is not present in an database or if it works poorly, you can transfer references in other ways: via importing a file you have downloaded on your computer or connecting to a database from within EndNote (see sections 3.4 and 3.5).

We show you the direct export possibility for the Web of Science and PubMed databases.

Web of Science
A link to Web of Science can be found on the homepage of the University Library.

Here you can do a search. A screen with results looks like this:

At the top of this screen you see: “Export”. Open this menu and choose “EndNote Desktop”:

Here you can fill in the number of records you want to save. You can also choose the fields you want to work with.
It is wise to choose “Full Record” (but do not mark “Full Record and Cited References”):

If you click on “Export”, EndNote will start and you can choose the library in which you want to place the results.
Click on Open and the data will be saved. It is also possible that EndNote does not open but a file is downloaded on your computer.
Now open this file, EndNote will be started and the results will be saved.

After saving you see the new references as a separate selection.

You can make all references visible in your library via All References on the left side or at the top via References – Show All References.

You can also mark references in the Web of Science by filling in the small boxes (see the screen above).
You can save them via “Add to marked list”. On top via the tab “Marked list”, you can export the selected records to EndNote.
Here you can select precisely which data you want to save.


Also in PubMed direct export to EndNote works well.

A. Export only one or a couple of references

  • Have a look at the articles found in PubMed and export relevant references (one by one) via 'Cite', displayed below each article    
    Click on 'Download .nbib'. Click on 'Open' at the bottom of your browser (or double click on the file), and the reference will be automatically send to your EndNote library.
  • Alternatively, you can select relevant articles in the results list in PubMed and save them to the Clipboard.
    Via Send to (below the search bar in PubMed) > Clipboard
    Articles on the Clipboard can be exported to EndNote in one go, via Send to > Citation Manager (see option B).

B. Export all search results at once

  • Click Send to (below the search bar) > Citation Manager
  • Selection: choose whether you want to download all results (All results) or only the references you have selected (Selection). It is possible to download a maximum of 10.000 references at once.
  • Click on 'Create File'.
  • The .nbib file will be downloaded.
  • Click on 'Open' at the bottom of your browser and the references will be automatically sent to your EndNote library.

Assignment 2

Assignment 2: Direct export from Web of Science

You can do this assignment after section 3.3

You can only do this assignment if you have access to the Web of Science (on campus; off campus employees and students of RU and Radboudumc can log in).
Also the EndNote program should be installed on your PC.

  1. Go to the Web of Science (can be found on
  2. Search for nursing homes and Netherlands or a subject of your own choice in the Web of Science.
  3. At the top of the search results you see: 

    Open this menu and choose EndNote Desktop.
    Then choose “All records on page”, and “Full record”.
  4. EndNote will now open and you can import the references in your library.
    It is also possible that a file is placed on your PC; you must click on that file to open EndNote and to import the references.


Have a look at your library:

  • Have the references been imported correctly?
  • Did all the data end up in the right EndNote reference field?
  • Do the references have the correct reference types?