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BibDesk to Word: Integrating References

January 19, 2011 Leave a comment

BibDesk Applescripts

OSX: Bibliography managers

Managing bibliographies, papers, the corresponding PDFs, matching metadata from Google Schoolar, IEEEXplore, CiteSeer, Web of Science, etc, can be a really frustrating (infuriating?) task.

I write most of my scientific papers in LaTeX (and I also did so for my PhD thesis), using the nice TexLive/MacTex distribution for OSX, which includes not only the Tex libraries and compilers, but also an editor (TexShop), a bibtex manager (BibDesk), a really nice equation editor (LaTeXit – this can even be used with MS Word or Apple Pages – see LaTeXit documentation), among other assorted and LaTeX related tools.

However, while managing bibtex files is quite simple (and made even simpler and snappier with BibDesk – I did it that way for my PhD), it still lacks a way to simultaneously find, match and manage the corresponding PDFs from the most well known reference services available (most of them requiring a paid subscription) in the internet (luckily all universities in Portugal have access to most of those services by means of the b-on initiative – that’s a good use of portuguese tax payers money! ;-)).

So, I’m looking for a swiss-knife solution for my bibliography needs, which can fulfil the following requirements, in order of importance:

  1. Import/Export bibtex, so I can use it with LaTeX, and also provide an open and simple and standard bibliography format that does not get obsolete over time;
  2. Provide a nice GUI for adding and managing references to the bibliographic database, where the metadata can be conveniently input and queried;
  3. Have the ability to search for papers from the GUI, using the most well known reference databases available in the internet (IEEEXplore, CiteSeer, Google Schoolar, JSTOR, ACM, Web of Science, etc), and get the correct bibliographic metadata;
  4. Have mechanisms to facilitate the retrieval of the PDFs corresponding to the papers in the database using the web services mentioned in the previous point);
  5. Manage my papers PDFs in a iTunes like fashion, so that I can always find the PDFs in my harddisk, using the GUI as a query interface;
  6. Provide some way to cite in MS Word 2008 and Apple Pages 09 (yes, some times, mainly when writing grant applications, project deliverables, and other boring paper work, I’m forced to use MS Word, or, if possible, Apple Pages);
  7. Allow to perform annotations in the PDFs (although this can be easily done using an external application like the Preview app of OSX or Skim)

An interesting application I recently found that somehow fulfils some of this requirements is Papers. It allows to import my bibtex bibliography (although I’m getting some minor issues with this) and then easily look for the PDFs of each publication using Papers internet search services. It then automatically manages the bibliographic data (which can be exported back to several formats, including EndNote format, bibtex, among others) as well as the PDF files, in a very similar way to what iTunes does for your music collection.

There seem to exist other alternatives to Papers, like SenteBookends and the infamous EndNote, which although not being all the same and each package having unique abilities, they all provide a range of similar features in the end of the day.

I’ve actually installed trial versions of Papers, Sente and EndNote and I’m trying to see which one suits my needs the best.

Regarding Pages, there exists a quite simple way to export a selection (or the entire set) of papers from the database to MS Word 2008, which then uses the internal Word bibliography features to create citations and bibliographic lists, avoiding the need of any other software package (like EndNote). In case you find MS Word 08 citation styles limited (which they are – only 5 are provided!), there is a way to “install” additional styles of citation. With this, MS Word finally becomes somewhat usable for scientific works. 😉

Another nice feature of Papers (and Bibdesk) is that  when you export the bibliography in bibtex format, and open it in Bibdesk, the PDF files you attached in Papers (and keywords) show up in Bibdesk (check more info here).

Sente already provides a proprietary mechanism to work directly with MS Word 2008 (not sure about Apple Pages though), and EndNote provides a Cite-While-You-Type (CWYT) feature (for Word 2008 and Pages 09), which I think it’s only part of the package that justifies installing it (EndNote is really ackward and suffers from bad software design…).

Finally, there is a new contender in the game, which is Mendeley, which allows you to manage your publications online (something I really do not feel the need at this stage), and even has a desktop version (but that still lacks most of the requirements I listed above).