Bibdesk: A free bibliography management application

For all of us who had one day to write a report or even better a thesis, managing the references is always more or less a nightmare. Of course, expensive software like Endnote of Reference Manager can do it. However these applications are only dynamically linked to Microsoft Word. As long as there is no simple to use software managing bibliographies for OpenOffice.org (this feature should be added in the next 3.0 version), LATEX is still the only way to write scientific papers, containing tables, figures, numbered equations and references, for free. Bibtex is the standard format to introduce literature references and thus Bibdesk is a good alternative to the above mentioned commercial software titles.


Introduction to Bibdesk

Bibdesk consists basically of a graphical frontend for Bibtex files. For the majority of us who use Latex, it is easy use since its native format is BibTeX, the usual format Latex uses to cite and format references. So all your already written .bib files will open flawlessly under Bibdesk. It is completely compatible with OS X 10.4, references appear in Spotlight, allows you to write Applescripts, and looks good (hey I concede that it is quite important for me . . . ). Bibdesk is also a way to manage your files even it you don’t mean to use it for scientific publications, as it allows you to link the .pdf ( or any other format) file of each item of your ’digital library’ . The best of all the features about Bibdesk is that it is completely free. Lots of people don’t use Latex because they don’t like to type code and they want a nice interface. Bibdesk helps with both, as it prevents the user from having to type Bibtex code (Figure 2) in addition to the nice interface.




Import and export features

There is nothing more boring than typing in information for all the fields related to a publication. Bibdesk handles this for you as it is able to read the files you download from ScienceDirect, Web of Science or any other scientiific web database. It also knows how to import data from other software such as Endnote or Reference Manager, and most of the other software export to the Bibtex format anyway. Unfortunately you will always have colleagues who don’t know about Latex or Bibtex and Bibdesk wi ll export to most of the other software formats for references. If by any chance you work with someone who only uses very basic features offered by modern computers, you can even export the formated citations to an HTML page. Bibdesk doesn’t present any drawbacks in this regard.




Managing references

Once the references are imported into Bibdesk, they have to be assigned a CiteKey which will be the string assigned to the publication in order to cite it in Latex. This can be done automatically by pressing command-K. Additionally, the format of the CiteKey can be defined in the Preferences of Bibdesk. Bibdesk allows to categorize files between articles, books, webpages, conferences etc. All standard Bibtex categories are supported. The needed fields are coloured in red, you don’t need this if you import from a web base but it unfortunately happens from time to time that one has to fill the fields by hand. Usually, even the abstract is imported.





Each publication can be linked to a .pdf file or even to the html address of your favourite database. A double click on the little pdf icon directly opens the file under Acrobat Reader or Preview or use the View in Drawer features to visualise the document directly in Bibdesk.

Cite while you write

While you are writing a paper, just highlight the references you want to cite in Bibdesk, right-click, choose ” Copy \cite TeX command for...” and you get the Latex command \cite{...} ready to be pasted. You can even ”Copy Text for...” and get something similar to this :


[1] ST Beckett. The science of chocolate. RSC publishing, 2002.


One drawback of Bibdesk is its compatibility, while extremely powerful when combined with a Latex frontend such as TeXShop, this feature doesn’t work with any word processor. I personally use Latex and thus it is not a problem for me, but if it could be linked with OpenOffice.org, this tandem would definitely offer a more general alternative to Microsoft+Endnote. Hopefully this feature will be incorporated in the future or that the built-in bibliography module of OOo 3.0 will be as good as Bibdesk, in terms of engineering and human interface.

To conclude this review, I would say that Bibdesk is probably the best Bibtex frontend available for the Mac OS X available at this moment. Its features are very close to other referencing software such as Endnote. If you use Latex search no more, this is a killer app. If you are an OOo user, you can look into b3, an open source Java application close to Bibdesk which is compatible with the free office suite.

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Link

Bibdesk may be found at http://bibdesk.sourceforge.net/.

thanks, and additional comments

As one of the BibDesk developers, I thank you for the kind review! Additionally, there are a few other features that I'd highlight:

- Reference autocompletion in Cocoa text editors (e.g. TeXShop, iTeXMac) via an input manager, that shows a popup list directly in your editor
- AppleScript support has enabled LyX and BBEdit integration for reference insertion
- We recently made the export support much more flexible, and you can export custom references as HTML/RTF/XML via templates
- Service for inserting formatted references in a text editor
- Automatic moving of linked files, as in iTunes/iPhoto, with very flexible naming
- Local network sharing of bibliography files
- Smart groups, category groups, and static groups

For more info on any of these, join the bibdesk-users mailing list or check BibDesk's online help.

BibDesk vs. CteULike?

Interesting article, thanks!

I'm now going to have to give BibDesk a decent workout.

I've just recently started using the free site CiteULike (http://www.citeulike.org) for managing references online, and am very impressed with it.

While I like BibDesk's concept of having your local PDFs linked directly from within the app, I absolutely *love* CiteULike's one-click reference field populator for articles from certain common publishers.

Does BibDesk have any plans for features such as this one, or perhaps even hooking into CiteULike's (RESTful, AFAICT) API?

easy to switch?

Thanks for this very informative review. Unfortunately, it is the second time that I want to give it a go, and for the second time I don't find the way to import my bibliographies from Endnote. Does this feature really exist or is there an indirect (export from endnote / open with bibdesk)way?

import from endnote

See http://bibdesk.sourceforge.net/wiki/index.php/FAQ or BibDesk's online help.

help with endnote

Apparently Endnote bibliographies don't export correctly into BibTex, but help is at hand: there are several suggested solutions at this page. Saved me a lot of hair-tearing.

BibDesk Styles

I've been trying to switch from EndNote to BibDesk--BibDesk is much more intuitive and has a much better design. I especially like the smart groups feature. However, I am having trouble using other BibDesk reference styles (e.g., apalike2 or nat, ect.) not included with my original download (or that aren't found, though they may be in other folders).
I have found a wealth of styles from CTAN, but am having trouble setting them up. The .bst files go in one folder (on my computer, I beleive its Library/teTex/share/texmf.tetex/bibtex/bst/base, but I could be wrong) and the .sty files goes elsewhere (where, I don't know). I think BibDesk would be perfect if I could add the necessary formatting styles instead of using EndNote (which already has them). Can you provide any info on where to move these and any other necessary files? Afterwards, it should be as easy as entering the style name under the preferences.
I appreciate you help,
From Maryland,
Kelly

Adding BibDesk styles

I am having the same problem.

Is there anyone who has managed to add new bibliographic styles to BibDesk?

Örjan Smedby
Linköping, Sweden

BibDesk trouble

Forgive me for posting a question here, but I'm positively out of ideas how to tackle this.
I have 2 items in BibDesk library: 1) proceedings, 2) inproceedings that cross-references 1).
No matter how I try to export a reference to 2) it gives me both of them 2) referencing 1). This is crazy. I couldn't find anything on how to fix it. Merge them together? I don't want to, they are semantically different.
Thanks.

Adding BibDesk styles

Do you mean the bibliography style in the document? If so, you need the .bst file which accompanies the style you want to use. The file has to be kept in the Latex document folder (or the path has to be referenced). It is called using \bibliographystyle{nameofbstfile}