Word processor support in citation managers: Is there a better way?

Citations of the relevant literature are an essential feature of scientific papers. Reference Manager software helps adding these citations and creating a bibliography. Are there differences in how reference managers work together with your word processor of choice?

Support for your favorite word processor

Support for word processors other than Microsoft Word is spotty. The Mendeley plugin is only a few months old, and the latest Zotero release (1.5b) broke the plugin for Word 2004. I expect the Word for Macintosh support of both these tools to become better over time. Google Docs doesn't have any reference manager integration. This greatly limits its usefulness for writing scientific papers. The RefWorks plugin connects to an online database, so you can't add or edit references without an internet connection.

Most word processor plugins add an extra menu that allows to add and edit citations (allowing the user to search the reference manager database), and to add and edit bibliographies (allowing the user to pick a citation style, see below). Most reference managers also allow scanning for reference tags in documents produced by other word processors (e.g. in the .rtf format), but that process requires a few extra steps.

Support for your favorite journal
I think it is very unfortunate that paper authors have to deal with a large number of different citation styles. All that we really need for paper references is the DOI (e.g. doi:10.1038/455708a) to make the reference automatically identifiable and some basic information (authors, title, journal, year, issue) to make the reference readable. But it is beyond my understanding why anybody would care about formatting details such as whether the pulication year appears before or after the journal name. There have been initiatives to standardize the formatting of references (e.g. Citing Medicine), but for now paper authors have to format their bibliographies in the style required by the journal. Citation styles are an important asset for those that write reference manager software. Many people will recall that Thomson Reuters (who makes Endnote) sued George Mason University (who makes Zotero) last year, because Zotero added a feature that could convert Endnote .ens citation style files into Citation Style Language .csl files. Mendeley is also using .csl for citation styles.

Is there a better way?
Word processor plugins are fragile and usually break when a new software version is released (see for example this chart for Endnote and Word for Macintosh). Native word processor support for references allows a much tighter integration into the word processor interface. Lastly, documents produced by different reference managers are not interchangeable, as each plugin uses a slightly different formatting approach. This means you can't write on a paper using Endnote and send it to your coauthor who uses Zotero.

The latest versions of Microsoft Word (2007 and 2008 Macintosh) have built-In support for citations and bibliographies, but this feature is severely limited for the requirements of academic papers. Only a handful of citation styles are supported, adding more styles is possible but requires some serious skills in XML editing. References are stored in one flat file (Sources.xml) and can't be searched. OpenOffice is also struggling with built-in bibliographic support.

LaTex has long included support for references using BibTex and shows how citation support should be done. Tools like JabRef or BibDesk extend this functionality, and most reference managers will import/export bibtex files.

Both Microsoft Word and OpenOffice should open up their citation APIs to third-party tools. This would create better citation tools, allows the easier exchange of documents between authors (journal submissions), and would it make easier for smaller tools such as Papers to integrate with word processors (a workaround is described here). If they wait too long, we will probably see the online word processors such as Google Docs, Zoho Writer start adding an API for citations and bibliographies and all of the sudden become very serious alternatives for writing scientific papers. Lemon8-XML already has very good bibliography support.

P.S. Bruce D'Arcus has recently come to similar conclusions (The Babel of Citations).

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4 Responses to Word processor support in citation managers: Is there a better way?

  1. Christina Pikas says:

    Sorry to keep harping on this – but your information on RefWorks is old. You *can* work offline using Write n Cite III. You download your database to the desktop and then can work offline. You can’t enter or edit records, but you can search and sort, add references to documents, and format bibliographies. As I said before, you can also use RefWorks with open office you just either manually or using one line cite view enter {{ref no}}, then run the document thorugh the bibliographic function online.

  2. Ted Erickson says:

    Thanks for taking the time to look into other software aviable and write it up. My lab has largely been using Endnote, but will have to look into other options due having a similar feeling that there needs to be a better way. I would also say at least for Endnote that it is not intuitive especially downloading citation from pubmed/scifinder. I will have to do a write up it. :)

  3. Martin Fenner says:

    Christina, thanks for the update. But the offline solution for RefWorks with Write N Cite III really is a workaround. Offline access is currently not available to Mac users, and you not only can’t add or edit publications (which is not that important since you are offline), but also don’t have access to PDF files stored in the online version of RefWorks (or so it seems to me). I also want my references and the associated PDF files on my computer for a variety of reasons, including the option to do fulltext searches of PDF files. Syncing as in Endnote, Zotero and Mendeley is really the better solution.
    “These MIT pages”:http://libraries.mit.edu/help/refworks/openoffice.html explain how to use RefWorks with OpenOffice.

  4. Andrew Sun says:

    Reference is not only about papers. What make latex good is its equal ability to manage figures, tables, chapters or any elements in a (cross-)citable manner.
    Figures and tables are often misplaced in Word. Latex provide a definite control on the appearance of these elements.
    However, one trend is possible, that as the Internet develops, we will eventually throw away the old publishing tradition that Latex meets precisely well, and the looseness of electronic texts will be the only formal need. Maybe that’s why things like Word never develop themselves for the true publishing need.