Once in a while I need to convert an EndNote library to a BibTeX library. For some reason this is much more difficult than it needs to be, and I always forget about how it c/should be done. I thought I wrote a blog entry about this the last time I struggled with it, but since I couldn’t find it I decided to write it up once again.
The process is based on using EndNote X2 on OSX and converting to a BibTeX file using the excellent free Bibdesk bibliography manager.
Open EndNote and Select the BibTeX export in Endnote
There is a BibTeX export template in EndNote, but for some strange reason this does not output a valid BibTeX file. However, to make things easier for ourselves, we will start from this template. If you don’t want to do these steps yourselves, you can download and see if the file I have created works for you.
Open the edit pane for the BibTeX style export
What we want to do is to tweak the template file, and this can be done by opening the template editor in EndNote (it would have been much easier to do this in a text editor, but the EndNote templates are stored as binary files…).
Open the template part in the edit pane
In the editor, find the “Templates” part.
Edit the template
1. Remove “label,” in the first line.
2. If you have written “research notes” in EndNote and want to use them with BibDesk, you need to add those to the template, by adding a line for “annote”.
3. Save the template and go back to EndNote.
Export the library
From the “File” menu, select export library. It should be exported as a text document using your altered BibTeX style. Unhook the “export selected references” option to export the entire library.
Rename the library to .bib
The file exported from EndNote is called .txt and should be renamed to .bib before being imported into BibDesk.
Import the library in BibDesk
Use the “open using temporary cite keys” to open the exported library. This is the trick to make it work, since we removed the labels when exporting the file from EndNote.
Ignore error messages
You will most likely run into some parse problems, but just klick “keep going” to ignore these.
Generate new cite keys
It is better to let BibDesk generate new cite keys for you, to avoid any further problems.
Now it is probably time to check that nothing was last along the way.
Alexander Refsum Jensenius is a music researcher and research musician living in Oslo, Norway. View all posts by alexarje
1. MIT does not offer a site license of EndNote. You can purchase and download EndNote from their website; students discounts are available. EndNote is available online for free to MIT users through Web of Science. From Web of Science, click the EndNote link at the top of the screen. Note, the online version has more limited functionality than the Desktop version.
2. Import citations into EndNote by exporting them from a database or by using a connection file.
Export options will vary by database so look for an Export option and EndNote or .ris format.
Connection files allow EndNote to search and import references from within EndNote. They only work with selected databases.
- In EndNote, go to Tools and Online search
- In the Choose a Connection box, select a database and click on Choose. This will display a search form for that database.
- Do a search. Highlight a citation. Right-click on it and select Add References To and add it to a group.
3. When writing your paper in Word, use the EndNote tab to insert citations and a bibliography.