Using EndNote with LaTeX

September 1st, 2008 by james

For most academics, the standard reference management software is EndNote. It lets you keep track of all the journal articles, books, web sites, etc. that you have read and might want to cite in your papers, integrating easily with Microsoft Word to create properly formatted citations and bibliographies.

But what do you do if you use LaTeX not Word to write your papers? Traditionally BibTeX comes to rescue. It uses a formatted plain-text file to store references and with the custom-bib and natbib packages, creating citations and bibliographies is fairly painless. You can even use a graphical editor like JabRef to help manage your BibTeX database.

However there can be problems when collaborating with people who use Word. How do you share your BibTeX references with EndNote users or vice versa?

My approach is to use EndNote as the master database for managing references. This lets you easily integrate with Word if necessary and you can still take advantage of the connection functions to retrieve references from your university’s library or other indexing services. However to share references between EndNote and LaTeX, you’ll need to follow these steps:

  1. Set EndNote to use Unicode. Go to Edit > Preferences… > Display Fonts and set both display fonts to a Unicode font, like Arial Unicode. EndNote already uses Unicode internally; this just makes sure that what you see is what you get.
  2. Label all your references with a unique identifier. You must use the “Label” field of each reference for this. I tend to use something like “Smith2000″ as these labels should be intuitive for later citation within LaTeX.
  3. Export the references using the BibTeX Export style.
    1. Activate the export style. Edit > Output Styles > Open Style Manager…. Then tick the BibTeX export style. Close the style manager.
    2. Select the BibTeX export style from the style drop-down at the top of the main window.
    3. Select all references in your library. Right-click on the reference and select Show All References if available. Click on any reference and press CTRL+A to select all references.
    4. Export the references by selecting File > Export… and choosing a destination. This should be the same directory as your LaTeX source file. By convention BibTeX files have a .bib extension so you might like to call your file something like refs.bib
  4. Tell LaTeX to use Unicode. Do this by adding \usepackage[utf8]{inputenc} to the preamble of your LaTeX document. This will tell LaTeX to process any accented characters in your main file and reference list correctly. Incidentally if you need to edit your exported *.bib file at any time, make sure you use a Unicode compliant editor like Notepad2. Otherwise any accented characters in your references might get messed up when saving the changes. Within the main LaTeX document you can still use LaTeX code such as \"{u} for ü or, if using a Unicode compliant editor (i.e. NOT the otherwise excellent TeXnicCentre), just enter the character directly.
  5. Use natbib and cite your papers as normal. Follow the instructions for using the natbib package and cite your references using the labels added above, e.g. \citep{Smith2000}, and something like


    to generate the bibliography (where refs refers to the refs.bib file saved in the LaTeX source directory as noted earlier and plain is a BibTeX style file – see this page for more info.

  6. Compile as normal. i.e. run LaTeX, BibTeX, LaTeX, LaTeX. See the previous link for details.

If you have a lot of references already in EndNote, it can take some time to set up the labels properly. However once you start using the system, it’s easy to maintain; you can add references, label them and export to a new BibTeX library in seconds. I should also add that this is mainly a Windows-specific fix; perhaps someone else can shed some light on what to do for a Mac. (If you and your collaborators write exclusively on Linux, then lucky you. No Word to worry about!)

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8 Responses to “Using EndNote with LaTeX”

  1. charlieNo Gravatar Says:

    how about the converse problem of using bibtex and word? I use bibdesk, the excellent bibtex library manager for macs, but have to do hand-referencing when collaborating with people using word… any suggestions?

  2. PierfrancoNo Gravatar Says:

    I use a Mac and my master database is managed with Zotero, the free extension to Firefox (any platform) realized by the Center for history and new media at George Mason University ( that has many advantages among which in my opinion at least these 7:
    1) it is integrated in your browser: precisely the same tool you use for connecting to catalogues and A&I services and then you don’t have to use two different applications;
    2) it has filters for a lot of online databases and catalogues, so it is able to import authomatically the records in a large number of formats just with a click of the mouse
    3) it can also retrieve and store the full text of the retrieved bibliographical items, whether they are PDF, html, or doc files, while in other databases like EndNote (if I am not mistaken: certainly older version of EndNote couldn’t do the job) you can just insert links to html pages or to internal files stored on your Hard Disk, but you had to do the entire job of downloading and linking yourself
    4) it has a function of using it with both MS Word and OpenOffice Write
    5) it can export its records in a number of formats, among which BiBTeX (also RIS; Refer; etc.).
    6) It can perform fulltext searches on the full text of the items it stores: PDF, HTML etc.
    7) it is a open source project and there is a lively forum. As in the case of other open source projects its user population can improve it a lot by sending requests, messages signalling bugs etc.
    So, my workflow is the following: since I use LaTeX for my papers (actually through LyX for MAC), I retrieve items from the Internet using Firefox + Zotero. When I write a paper I build a bibtex database using BibDesk (the free application for the MAC) and I fill it with the first importation of the records which I have previously selected and exported from Zotero (successive importations of new records added to the same bibtex database will also be possible, of course). The importation function is very easy: you can perform it just with a drag and drop of 1 to any number of Zotero records into BibDesk! Or you can do a batch import in the case of a consistent number of records
    There is also a script for importing records authomatically in both Zotero and BibDesK through a single click of the mouse from Firefox.
    Zotero can’t be used directly with LaTeX (and EndNote either) but it is recommendable for the features described above and also for sharing records with other people, whether they use Word or LaTeX since you can send them records in their preferred format.
    I could also add that the import function of Zotero from online tools opened in a Firefox window is recommendable because you don’t have to set specific channels via Z39.50 for each specific database and catalogues. So the bundle Zotero + BibDesK is a very effective choice. And completely free of charge, which is not the case of EndNote, a very expensive application. Another popular commercial application for managing bibliographies, that is RefWork, appear to have the same limitations of EndNote. So why not exploiting the several advantages of using just open source applications supported by large communities of users, which is the case of both Zotero and of course LaTeX? The way open source communities work is very important for ensuring much more flexibility and speed in incorporating new technologies, which is such an essential ability nowadays for adapting to the ever changing panorama of digital technologies. The same speed and flexibility is much more difficult to find in commercial applications.

  3. jamesNo Gravatar Says:

    Thanks for the tip on Zotero. I tried it briefly a few months ago but never got around to importing my current library (700+ refs). However free is good and it sounds like a solution for those who don’t have Endnote provided by their employer. Zotero might also be the solution to charlie’s Mac question as well.

    By the way, I forget to mention that when using the method above you might want to create a new copy of the default BibTeX export style, removing all of the notes fields from the template. Some style files, particularly those for Elsevier journals, included the notes in the output when you really don’t want it.

  4. PierfrancoNo Gravatar Says:

    Thanks for the practical suggestion about editing bibtex records in case of annotations etc. Just a few more comments about the Zotero EndNote comparison I have proposed. To be honest, I think that a full comparison of the two applications would be useless at the moment and also unfair. This is because folks at George Mason University are working at a major enhancement: that is the possibility of storing online one’s own Zotero bibliographic records in a public folder and share them with others, just as online-only applications such as Connotea or CiteULike do, but with the major advantage of having also a local copy of one’s own bibliographic database, which RefWorks seem still unable to offer, at least at individual subscribers, since it is just an online database. This feature will really make sharing records very easy.
    I could also add that at the moment Zotero doesn’t provide important features which EndNote and RefWorks offer, like the ability to do a global edit on a given set of records, or a good interface for working on subject tags, or even the ability to edit authors’ names in order to make them unifor and consistent. However, as I said, the group working at the project has surely a long list of improvements planned in the near future. Above all Zotero has the unvaluable advantage of working “inside” the browser. What we can read in today’s Official Google Blog message “A fresh take on the browser”, that is that Google’s engineers “spend much of our time working inside a browser” is true for everyone of us.

  5. darioNo Gravatar Says:

    As a Mac user, I use the applications bundled with the MacTeX distribution (incidentally, MacTeX 2008 is on its way!). These include Bibdesk, a fantastic reference manager using bibtex as its native format and well integrated with TeX frontends such as TeXShop (here’s a description of my TeX arsenal).

    I have the same problem as Charlie when collaborating with Windows/Word users. In this case I manually copy my references in the Word document, using the appropriate output filter.

    There’s a sourceforge project called BibFuse consisting of “applescripts for integrating BibDesk with Microsoft Word in Mac OS X. They allow non-destructive creation of bibliographies that draw their data from BibDesk publications”. I haven’t checked this out yet (I’m not a big fan of AppleScript), but I’m willing to give it a try if someone else found it useful.

  6. PierfrancoNo Gravatar Says:

    About the issues of the collaboration between the LaTeX and the MS Word communities: perhaps it is interesting to know that Zoho, the online office suite available for free at Zoho and whose aim is to support online collaboration, makes it possible to upload .doc files and download them authomatically converted in other formats, among which LaTeX. You can then open these converted LaTeX files using your LaTeX editor, for example TeXShop (MAC users), and process them: the result is a pdf like the original Zoho file.
    Unfortunately at the time Zoho doens’t accept LaTeX file (don’t know why, given that they are able to convert files into this format for the download).
    Another way for exchanging bibliographic records between the two communities is using the same reference manager: besides Zotero and the online free database CiteUlike, there is JabRef, freely available from JabRef. It can be installed on PC, MAC and Linux computers. However for exchanging it is enough to use the same export format: the more widely used is the RIS format (also known as Reference Manager Format), which has become a sort of ‘lingua franca’ for reference formatting software.

  7. MatthiasNo Gravatar Says:

    At my scientific institute, we were also seeking for a solution that lets us manage & share a common pool of academic literature, and that would be useful for both, LaTeX and MS Word users. We also wanted a solution that would allow us to dynamically update our institute’s online publication lists from the same pool of bibliographic data. Since (back then) we couldn’t find anything like that, we developed our own open-source solution (refbase).

    refbase supports import from many formats & databases, export to common bibliographic formats (such as EndNote, BibTeX, RIS or XML formats for OpenOffice & MS Word), and can make formatted lists of citations (as PDF, RTF, LaTeX, Markdown or plain text).

    Besides, refbase offers powerful search features, RSS support, and APIs (such as SRU/W, OpenSearch & unAPI) for machine-based retrieval. Its support for unAPI and COinS metadata allows tools such as Zotero to automatically sense & retrieve bibliographic metadata. There are also command line tools to automate search & retrieval, import or the synchronization with a local BibTeX file. And apps such as Bookends (for the Mac) offer a direct “Upload to refbase” functionality from within the program.

    At our institute, we use an online refbase database as our master dabase — this allows users to choose the tool of their choice (EndNote, LaTeX/BibTeX, plain MS Word, etc) when writing their papers.

  8. AmrinderNo Gravatar Says:

    Ha, I used to struggle with the very similar problem of trying to export from EndNote to Bibtex. There are a few downloadable tools that can do the task, but a much simpler web page is at:

    Free, and nothing to download/register.

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