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EndNote 21 Basic course

3.5 Connecting to databases from within EndNote

What is a connection file?
A connection file is a piece of software that allows you to connect to a bibliographic database from within EndNote. Without leaving EndNote, you can search the bibliographic databse and transfer references to your EndNote library.
Not all bibliographic databse support this feature.

Hundreds of connection files are supplied by EndNote, but often these are not usable, because the bibliographic databses are protected. You can however use connection files supplied by EndNote for publicly accessible databases such as PubMed.

If you work with EndNote off campus you must make some adjustments (once-only), so you can access the database off campus too.
This is what you must do:

  • In EndNote go to “Edit” – “Preferences” – “URL & Links”
  • Replace “ISI BASE URL” by
  • In “Preferences” go to “Find Full Text”. Tick all the options.
  • At “OpenURL Path” fill in:
  • At “Authenticate with URL” fill in:

Working in EndNote with a connection goes as follows:

Look on the left under "Online Search". Bibliographic databases may already be listed there. You can use those.
Or click on the +-sign which will bring you to all bibliographic databses you can access.

Clicking on the +-sign will take you to all connection files for all accessible bibliographic databses:

You can choose a connection file from the list.
Select a connection file and click "Choose".

When the connection is established, an Online Search dialog box will open at the top of the screen:

Here you enter search terms, for example in the first entry field smoking cessation and in the second social support.
Also remember to select "All Fields" as fields instead of eg "Author" and "Year".

After clicking on "Search" the search will be performed and the search results found will be displayed in your library.

The references have not yet been transferred to your EndNote library, they are only shown. You can transfer them by selecting references (click on them and hold down the CTRL or Shift key if you want to select more than one).
By clicking on the numbers (25, 50, 75 etc.) above the references behind Retrieve results you can browse the (entire) set of search results.

You open a reference by double clicking it.

At this moment the references are not yet saved in your EndNote library.
You can save them by selecting references (click on one and hold down the CTRL-key if you want to select more).

After selecting click on the button to actually transfer them to your library.

You will then see it was successful at .



More about connection files
Like filters, connection files are not perfect. Therefore, check the references included in your library.

Some connection files such as PsycINFO (OvidSP) or Medline (OvidSP) ask for a remote password via a pop-up screen. If you first create a VPN connection, you can click OK in the pop-up screen without entering anything, after which the connection will work. .

Assignment 3

Assignment 3: Connecting to PubMed

You can do this assignment after section 3.5

PubMed is a widely used database for searching journal articles in the field of medical sciences.
The PubMed database is freely accessible. We connect to PubMed via the connection file which is included in the EndNote software.

  1. Open EndNote and create a new library.
  2. Use the connection file PubMed (NLM) in EndNote under Online Search to establish a connection with PubMed (or access PubMed (NLM) via Tools - Online Search).
  3. Search for references on nursing homes in the Netherlands (type: nursing homes Netherlands)
  4. Transfer the first 100 shown references into the newly created library.

Have a look at your library:

  • Have the references been transferred correctly?
  • Which fields are filled?
  • Do the references match the reference types?