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A blog by Rob J Hyndman 

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Managing a bibliographic database

Published on 2 August 2009

All researchers need to main­tain a data­base of papers they have read, cited, or sim­ply noted for later ref­er­ence. For those of us using LaTeX, the data­base is in the Bib­TeX for­mat and is stored as a sim­ple text file (a bib file) that can be edited using a text edi­tor such as WinEdt.

But it is often eas­ier to edit the file using spe­cial­ist soft­ware. My cur­rent favourite tool is JabRef. It is espe­cially use­ful when search­ing for ref­er­ences in a large data­base. How­ever, there are sev­eral things I would like to be able to do with my bib file, but JabRef doesn’t pro­vide the facilities.

First, when I save a pdf of an arti­cle to my local disk, I would like the bib details to be auto­mat­i­cally added to my data­base. But I cur­rently have to go and type them in myself. Usu­ally I don’t bother until I need to cite the paper, but then I have trou­ble try­ing to find a paper that I’m sure I’ve saved, but can’t find. Even Google Desk­top seems to have trou­ble find­ing papers that I’ve saved.

Sec­ond, it would be nice to share my bib file with my research stu­dents and post-​​docs. Cur­rently I have to send them a copy periodically.

Third, when I find a paper on Sci­enceDi­rect, or RePEc, or some other online repos­i­tory, it would be great if I could just click a but­ton and have the paper added to my data­base, along with a link to the URL where the paper can be obtained.

In the last year, there has been a lot of work going on in try­ing to develop new tools to solve some of these prob­lems. There are now tools avail­able to do almost every­thing I want, but no one tool does them all. Unfor­tu­nately, many of the avail­able tools are designed to work with MS-​​Word (ugh) and don’t inte­grate neatly with LaTeX/​BibTeX.

One of the most promis­ing of the new tools appears to be Mende­ley. I’ve tried import­ing my bib file into Mende­ley, but it seems to fall over with any­thing more than a few hun­dred items. My bib file con­tains about 3000 items. I’m told they are work­ing on per­for­mance issues for the next release, so I’ll look for­ward to try­ing it out again in a few months.

In the mean­time, I’ll stick with my tried and trusty JabRef, despite its lim­i­ta­tions.

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9 Comments  comments 
  • Min Liu

    I use zotero now, and I think it is convenient.

  • inwit

    First of all, it’s been a plea­sure to dis­cover your blog. Lots of use­ful infor­ma­tion here!

    Sec­ondly, I must say that Zotero works quite well, allow­ing you to do eas­ily the three things you men­tion in this post (link pdfs and bib­tex entries, one-​​click entry sav­ing and data­base shar­ing). Plus it has some other nice fea­tures, like the time­line, for example.

    Good luck!

    • http://robjhyndman.com Rob J Hyndman

      As far as I know, Zotero allows bib­tex export but not bib­tex sync­ing. So you have to man­u­ally export your Zotero library from time to time — not too much has­sle, but not the same as auto­matic sync­ing. There have also been issues with Zotero’s bib­tex key format.

  • Pingback: Managing a bibliographic database « Idyawati's Blog

  • http://kenmankoff.com Ken Mankoff

    You can have Zotero do bi-​​directional sync­ing with Zot2Bib http://​mack​er​ron​.com/​z​o​t​2bib/ so you can com­bine Zotero with Bib­Desk (if on a Mac).

  • Alexan­dra

    Hello,

    Many thanks for your use­ful and help­ful blog!

    I am very begin­ner for using LaTeX. I wrote my the­sis in Word but want to re-​​write it. My bib­li­ogr­phic is in End­Note. Is there any way to trans­fer an End­Note files to wher­ever LaTeX can use? Sorry, my ques­tion probalbe is not cor­rect. So much I don’t know about LaTeX!

    Thank you.

    • http://robjhyndman.com Rob J Hyndman

      End­note will allow export to bib­tex format.

  • Loreto Bravo

    Have you tried 
    http://​www​.qiqqa​.com/? It keeps track of the pdfs you add and then helps you find the bibtex. 

    • http://robjhyndman.com Rob J Hyndman

      I haven’t tried it, but it looks like it does many of the same things as Mende­ley does.