EndNote at UCSD - For BML Users

EndNote is a popular software program for managing databases of citations. It is used to maintain personal or group "libraries" of references to articles, books, patents, and other publications. Authors use it with a word processor to format bibliographies and captions for publication. This page is provided to help with using EndNote with data from the main biomedical-related databases at UCSD. Similar pages from other libraries are available with information about other subject-oriented databases.

Because there are so many possible combinations of software programs, version numbers, operating systems, platforms and databases, this page may not answer your specific question. The software vendor is your best source for answers to specific questions about these programs, especially regarding any customization you may have made or wish to make.

Old version? If you are using a version older than 8, we recommend upgrading to the current version - it's much easier to get records in from online databases. The current version is X5.

End-Note Classes (Biomed focus):
EndNote classes are offered each quarter.  We offer classes in both the desktop and web-based versions.

To sign up please use our Class Registration Form

We also offer individual or group consultations to UCSD students, staff and faculty. We offer an online consultation request form. Or, you can just ask us a question by e-mail.

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PubMed & Endnote - printable PDF handout

Download/Import Method:

  • In PubMed:: With your desired records on-screen, change the Display to the MEDLINE display format. Then select Send to - File within PubMed and save the file to your local computer. Be sure to remember where you saved the file and what the name was.
  • In End-Note: Choose the PubMed import filter. If you use EndNote version 7 or earlier, you may need to get an updated Import Filter for Pubmed.
    Latest PubMed Import Filters: Windows - Mac

Connect Method:
In EndNote, choose Online Search (called Connect in older versions) and select PubMed (NLM).See the EndNote PubMed page for details.
Latest PubMed Connect files: Windows - Mac


BIOSIS (Thomson Scientific)

In BIOSIS: select your desired records. If you want specific parts of the record, first save your records to a marked list. There you can select the fields you want to capture, and then select one of the following output options:
Export to Reference Software: this will give you the option of opening the file with Endnote. Note, this feature only works if you are doing your search on a computer where EndNote is installed.
- or-
Save: use the Tagged display format. Save the file on your computer. Then go to EndNote and Import that file using the Web of Science import filter.
Latest Import Filters: Windows - Mac.

Connect Method: Thomson Scientific (formerly ISI), our vendor for BIOSIS released a Connect file in October 2007. If your version of EndNote is earlier than that, you will need to download this connect file and save it to the "connections" folder in your EndNote Program Files.
Windows version / Mac version.


PsycINFO via CSA

In PsycINFO: choose which citations you want to import. Select the Save/Print/Email button, and choose the record format you want. Tip: you might wish to check the "Omit Cited References" box - many articles have dozens of cited references which you may not want to have cluttering up your End-Note database. Choose Save or E-mail, and note the location of the file you save. There is no special format for End-Note - records are automatically saved with appropriate tags for End-Note to use.

In End-Note: Use the PsycINFO/Cambridge Scientific Abstracts import filter. This filter is fairly new - you may have to download it from EndNote's site: Windows - Mac.

Connect info for PsycINFO: The Connect file for PsycINFO that comes with EndNote needs to have UCSD's account information added to it in order to function. We have created a new Connect file for UC's PsycINFO for Windows users, right-click to save this file to the Connections folder within your EndNote program files. Mac users: please save this file to your Connections folder.


Web of Knowledge/Web of Science

In Web of Science: Select your desired records. If you want specific parts of the record, first save your records to a marked list. There you can select the fields you want to capture, and then select one of the following output options:
If you are working on the computer where End-Note is installed, click the "Export to Reference Software" button to launch End-Note. Select the database you want the references imported to and click "Open." This will place those records directly into End-Note.
If you are working on a different computer, choose "Save to File" or "E-Mail" instead of "Export" and this will give you a file for importing later.

In End-Note: if you used "Save" or "E-Mail," you can import records using the "ISI Web of Science" import filter.

Connect info for Web of Science: There is a Connect tool for Web of Science, but it does not work very well. Author searches in particular do not work reliably, and you cannot use the Connect tool to perform Cited Reference searches, which is what most people use Web of Science for. It works OK for known item searches, and works best to search by article title.



The best way to get book information from Roger into EndNote is to use Connect, aka Online Search. Use the title field and search for the exact book title.  Current versions of EndNote come with a connection to Roger. If your version does not have this, you should download it from the company website:

  • Windows right-click the link and save the file into your EndNote/Connections folder
  • Mac - you will need to browse the list to University of California San Diego (go to Last then browse back!) and save the file to your EndNote/Connections folder.

Alternatively, you can save and export records from Roger and then import them into EndNote using the "Innopac" filter but when you import them they will lose the call number information, so the Connect method is better in this case.


EndNote comes with an Import Filter for the University of California's Melvyl Catalog. If your version of EndNote dates before 2003, you will need to go to the EndNote "support" site and save an updated version of this file.


EndNote's Online Search Tool (aka "Connect")
EndNote can perform direct searches of many databases including PubMed, PsycINFO and others, without having to use the "native" database interfaces. This is called Online search (or Connect in old versions).  It is very handy for simple author or title word searches and for locating "known" items, but for complex subject searches, we still recommend conducting your searches in the original database and then exporting or downloading your results for use with EndNote.

NOTE: Off campus users will need to connect to the UCSD network via the Virtual Private Network (VPN) to use this feature with our commercial databases.   PubMed and Roger are free databases and don't require the VPN.

 OpenURL Information and "Get Full Text" feature

If you use EndNote X2 or higher and want to use the "Get Full Text" feature to grab PDFs, you should enable this. In EndNote 9, X, and X1, you can enter OpenURL information in order to add UC e-Links to records.

  • Go to Preferences (in Windows it's under Edit > Preferences)
  • Choose the option relating to OpenURLs - it's called OpenURL or URLs and Links depending on your version.
  • check the "Enable Open URL" check box. You need to delete the pre-installed OpenURL Path and type in the following:
  • In the Arguments box, replace "WoS" with "EndNote" so that the argument is exactly as shown in the image below. If there's nothing in the box in your copy of EndNote, you can copy and paste the following text to replace the entire argument. Be sure you don't have any spaces in the middle of this:

Here's what it should look like when you are done:

Updated: 5/11/2012

Friendly URL: http://biomed.ucsd.edu/go/endnote.htm

Bibliographic Software