Reference Management with EndNote and BibTeX

In this post I discuss how you can the balance the need for a reference management system that supports both BibTeX and Microsoft Word.

LaTeX documents generally make use of BibTeX or BibLaTeX for handling the reference management. The way that references are handled and dealt with in LaTeX is one of the reasons I was first drawn to LaTeX as an undergrad, and I think that it really is one the selling points of the system. However, while BibTeX excels at handling references within a document or a project it really doesn’t have the capabilities of storing references. Most people I know who use LaTeX simply keep one big master bibliography file and then simply copy the entries they need into a new bibliography when writing a paper that needs those references. Others don’t bother with this, but attaches the same master bibliography file with every publication – an operation that can make you really unpopular with the publishers I might add.

Stand-Alone Reference Managers

JabRef seemingly fills the void; the application stores references natively in a BibTeX format. However, JabRef does not seem to play very nice with Word. This might not mean much to most users of LaTeX, but coming from the humanities there is a very strong tradition for using Microsoft Word for basically anything from taking notes to writing dissertations and book manuscript (yikes!). There are even some journals that only accept submissions in a Word format. One of the more Word-friendly reference managers is EndNote. Especially, EndNote’s cite-as-you-write integration with Microsoft Word is very popular. As a consequence many of my colleagues (my self included) have over the years built our references libraries in EndNote.  EndNote has the ability to organize your references in different categories and subcategories. It integrates very nicely with Word, and you have the ability to attach external files (for example PDF’s) to reference entry. The latter means that I not only have all my references in one central database, I can read articles and book chapters (if available for download) without looking the entry up online. It also has the possibility of exporting entries to BibTeX, which is what we’re going to look at next.

EndNote LaTeX Integration

First, what we’ll do is download a new BibTeX output style from the EndNote website. With this new output style we can define the BibTeX key using an entry’s label field. Otherwise, EndNote will automatically assign it’s internal record number to the BibTeX key. This is not very helpful when sitting with your LaTeX document and need to remember which key is referenced to which record number. You can of course manually change this to a more useful key, but if you have 50 references you’d have to repeat this 50 times. Plus, since you manually change the output file the next time you need this reference you’d need to make this change again.

After you download the file you simply run it and open it with EndNote. In order to activate it you need to go to Edit -> Output Styles -> Open Style Manager:

This will open a new window. Scroll down to the line called “BibTeX Export using EN Label Field” and tick the box:

Return again to your library and double click on the entry your want to export and scroll down to the label field:

I usually like to name them according to first author and year so I enter “sacks1974″ in the label field

Then you select the reference you want to export and go to File -> Export and select the BibTeX Export using EN Label Field” option:

This will generate a text file that looks like this:

@article{sacks1974,
author = {Sacks, Harvey and Schegloff, Emanuel A and Jefferson, Gail},
title = {A simplest systematics for the organization of turn-taking for conversation},
journal = {language},
pages = {696-735},
ISSN = {0097-8507},
year = {1974},
type = {Journal Article}
}

This can then be copied directly into you .bib file.

“But I have 82 references!”

A potential problem is that exporting files individually can really take a long time if you have many references. Luckily there is a smarter way to go about this using EndNote’s categories. You can order all your references in ‘Sets’ and on the lower level in ‘Groups’. One entry can be in as many sets and groups as you like. So, what we’re going to do first is to create a new set called ‘Papers’. Go to Groups-Create Group Set:

We’ll name this ‘Papers’. Next create a new group within this set. This group will contain all the references that we need for a new hypothetical paper we’re writing, so let’s call it ‘myGreatPaper2017’. Now, we just add all the references already we need for that paper:

Make sure you’ve updated all the label fields. Granted, the manual labor is a pain, but at least we only need to do it once for each entry, regardless of how many categories you put your entries in. Now, instead of selecting an entry you select the group ‘myGreatPaper2017’ export the file to your working directory and save as myGreatpaper2017.txt. Instead of getting a file with one entry, we now have one file with all the entries we put into the category. You can as before open the file in an editor and copy all the contents to you .bib file or simply change the extension from .txt to .bib and add this file as you bibliography file in LaTeX.

With this workflow we have a somewhat easy way to generate a bibliography file for LaTeX documents, while still maintaining the ability to cite references from Word (oh the dread!).

I’d be interested in hearing from other LaTeX users how you manage your references, ensure LaTeX / Word interoperability, etc.

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