EndNote: PubMed Auto Export News


posted by cmethod | |

EndNote: PubMed Auto Export



Automatic export of PubMed references can be done using Internet Explorer (IE) or Mozilla Firefox browsers. Both browsers are available for Windows/Vista and Macintosh platforms. IE is the default Internet browser for Microsoft ( Mozilla Firefox, reputed more secure than IE, is widely used on both Windows/Vista and Macintosh platforms. Since Firefox versions 3.0 and above are already configured for automatic export. Note that these instructions apply to EndNote X2/X3 only.


The key to this automatic export process is in the browser setup. IE 7/8 require an adjustment to their default settings. The necessary adjustment is unavailable in older versions of IE.  


To configure IE for PubMed auto export to EndNote. To configure IE version 7:


·         Open IE 7

·         Click Tools

·         Click Internet Options

·         Select the Program Tab

·         On the lower right side click Set Program

·         Select “Associate a file type or protocol with a program” See Figure 1

·         Select .txt

·         Click Change Program

·         Select EndNote

·         Click OK, and EndNote should open.

·         Select the EndNote Library wanted

·         Highlight PubMed as the Import Filter, and click Choose



For those using IE 8, the settings are somewhat different.


·         Locate any text file (.txt) file on the computer, or create a brief test file (.txt)

·         Right click on txt file icon

·         Select Open With

·         Go to Choose Program

·         Highlight EndNote

·         Check box (Always use selected program to open file)

·         Click on Okay

·         Now any text file will be opened by EndNote


Note: if Notepad is needed, reverse the steps to make Notepad the default to open text files. If Notepad is used regularly for other applications, this option is not recommended.


If the user has administrative rights to the computer, there is another method of using IE8 in XP:


·         Go to Start

·         Choose Control Panel                                                                   

·         Choose Folder Options

·         Select File Types tab                                                                                                      

·         Under Registered File Types scroll down and choose txt

·         Choose Advanced at the bottom of the page

·         In Edit File Type menu choose Open and then Edit

·         Under Application Used to Perform Action, browse to Programs Folder on hard drive

·         Find the EndNote folder and choose EndNote.exe

·         (It will look something like this… "C:Program FilesEndNote X2EndNote.exe" )

·         Click Okay


In PubMed do the following:


·         Select references

·         Click Send To

·         Choose Destination File

·         Change the Format to MEDLINE

·         Click Create File

·         Choose Open

·         When EndNote opens, choose the PubMed filter


If the user has administrative rights to the computer, there is another method of using IE8 in Vista:


·         Go to Start

·         Choose Default Programs

·         Choose “Associate a file type or protocol with a program”

·         Highlight txt in the menu window

·         Click Change Program

·         Choose EndNote

·         Click Okay


For more assistance contact IUSM librarians Sue London , Carole Gall or Director of Educational Technology, Osman Gurdal .

975 W. Walnut Street, IB 100 | Indianapolis, IN 46202 | Ph: (317) 274-7182 | Fax: (317) 278-4506