Exporting Endnote, Mendelay, and BibTex databases to MS Excel

This is a basic guide for converting an EndNote database format file to Microsoft XLS or XLSX (Excel). 

Converting from EndNote to MS Excel is a far from trivial task as there is no single agreed standard database format for storing academic references. In addition, author fields can have single or multiple authors and this alone allows for a range of possible format options for saving.

The most direct methods are suggested here. However, I have never been able to get either method to work reliably with anything more than a few records at a time. All it needs to go wrong is a stray “tab” character somewhere in the data and the output is corrupted. For large data sets I found the fixed width output option far too time consuming to process, and with 1000+ record sets it became entirely impractical to verify the output quality.

The following method, while a little long winded, has proved extremely reliable for me (tested with data sets over 1,400 records).

Step 1: Export from EndNote to XML

In EndNote

• Highlight the records to export
• File -> Export
• Save as type: XML
• Output style: Show all fields
• Save (note where you are saving the file)

Step 2: Import XML to Mendeley

In Mendeley Desktop (free download)

• File -> Add files
• Select the XML file from Step 1 and Open it

This will import the file with the records properly formatted for Mendeley and you can see them in your Mendeley Library.

Step 3: Export from Mendeley to BibTex

In Mendeley Desktop

• File -> Export
• Save as type: BibTex (*.bib)

Step4: Open BibTex file in Jabref

In Jabref (free download)

• File – Open database
• Select the BibTex (*.bib) file from Step 3 and Open it

Step 5: Export from Jab ref to CSV

In Jabref

• File -> Export
• Files of type: Open Office CSV (*.csv) [There is an option for MS Office XML - I had less success with this format]

Step 6: Open CSV in MS Excel

In MS Excel

• File -> Open (Select “All Files” or “Text Files”)
• Select the Open Office CSV (*.csv) file from Step 6 and Open it
• This should open the converted files and you can now (File->) SAVE AS *.XLS or *.XLSX

As you can see it is a tedious route but, having tried several approaches I think this is the most robust and avoids having to go line by line through the outputs looking for misplaced fields. The added advantage is that if you have already invested in EndNote the other software is free.

It work but, a single step conversion tool would be welcome.