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Search 2: When I try to search PubMed or the Web of Science in EndNote using a connection file I get "No Matching References Found" when I know it should return some results or I get a time-out error message after two minutes. My computer uses a proxy server. How can I fix this?

Answer:

You can add the URL for the HTTP-based connection as an exception. To find the setting to change in your proxy server settings do the following:

  1. Click on the Edit menu > Connection Files > Open Connection Manager.
  2. Browse to the remote connection, highlight it and click Edit.
  3. Click on the Connection Settings option on the left of the screen.
  4. You will find the URL under Server Address. The standard address you will see here for 2 common sites are
    PubMed: www.ncbi.nlm.nih.gov
    Web of Science: gateway.isiknowledge.com
Windows
EndNote 5*, 6, 7, 8 and later use the proxy settings in the Windows Internet Options for HTTP-based connections such as the Web of Science, so make sure these are set correctly to recognize your proxy server.
  1. Open the "Internet Options" applet on the Windows Control Panel (or select Tools / Internet Options in Internet Explorer).
  2. Select the Connections tab and click the LAN Settings button.
  3. Make sure that the "Use a proxy server…" box is checked and that the address and port number of the proxy server are entered correctly.
  4. If the problems persist, click on the "Advanced…" button in the LAN Settings dialog. Under "Do not use proxy server for addresses beginning with:" type the URL of the site you are trying to search (either PubMed or Web of Science). Click OK and try the search again.

Macintosh OS X
Try adding the PubMed/Web of Science URL to the proxy exceptions list in your System Preferences.

  1. Open System Preferences and select Network / Proxies tab.
  2. Type the URL of the remote database under "Bypass proxy settings for these Hosts & Domains". Also make certain that "Use Passive FTP Mode (PASV)" is not checked.
* If you are using EndNote 3, 4, or 5, please note that these versions of EndNote are no longer able to connect to and search PubMed directly. Please click here for details on this issue.

This page was last modified on: August 27, 2008

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