Bibliography Reference Management with JabRef
Wednesday July 12th 2006, 13:50h
Filed under: ETH Zürich

One of the central tasks of PhD students is to manage literature; on the one hand for their own thesis, on the other hand for their prof’s publications. So here’s how I managed the technical part of this duty during the last 6 months at ETHZ:

  • I use JabRef, a great platform-independent open source software for bibliography reference management.
  • For anybody who is interested in similar areas of research, that’s my 164-publications-repository of papers about organization science, knowledge management, innovation management, open source software etc. (PDF only available on request)
  • JabRef has a lot of great features, one of them being a very format-open application with various import and export functions, saving the reference list database in the BibTeX format.
  • JabRef lets you also categorize your papers in multiple groups (see screenshot below), add the abstract to each reference and link the papers to their corresponding PDFs if locally available.
  • In the customized field workingstatusmatthias I write down why I referenced the paper and if I’ve already studied it (unfortunately most of the papers still lack this latter property ;)
  • To get an ordered and correctly formatted list of 130 references for a publication of my prof I searched for the bibliographic data, added the references to a specific group, copied them into a new JabRef database (idea by Christian Beermann) and exported them as a formatted RTF file.
  • Since the journal’s format guidelines are clearly defined I needed to create a customized export filter. Here it is, the almost correct JabRef RTF layout for references in Organization Science!
  • The only thing I couldn’t archieve yet is the particular author format Org Science requires: e.g. von Krogh, G., I. Nonaka, M. Aben, which is basically an abbreviated list of authors, beginning with the last name of the first author and adding the remaing ones in the firstname lastname-order. So it’s necessary to program this specific author formatter class in Java, add it to the source code/jar file and implement it in the Orc Science layout files. Anyone who has done this is warmly welcome to report it here ;)

Screenshot of my JabRef collection of publications

Update 2007-06-12: This week I had to export about 70 references according to MIS Quarterly literature format so I wrote a simple RTF JabRef exporter for MISQ.


14 Comments so far
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BibTex has an OrgScience template, so could that be used? Of course a bibliography pdf file is not of much use here…
(BTW first names do not need to be abbreviated as far as I know for OS)

Comment by spaetz 07.12.06 @ 15:57h

As i am not the most sophisticated person concerning such issues, i store everything in my head (and of course in a steadily growing BibTex file). If all else fails, there exists a huge database of high energy physics papers on the net which provides everything one could dream of.

Comment by furi 07.12.06 @ 16:55h

Hi there. At TIM (ETHZ) we are using Endnote, which is available at IDES.ethz.ch. We have made very good experience with this program, since it is easy to use and rather stable in use. Unfortunately, it does not support contextual work. You can download records from several databases such as Web of Science, NEBIS or Google Scholar. It is a suitable, small programm that helps you to write publications.

Comment by Andreas Biedermann 07.13.06 @ 7:05h

I just use vi for my references and love it because it does not require me to touch the mouse. Giving smart syntax indenting and highlighting plus a few keymaps, I can hardly see the need for anything else. I definitely would not use a Java-based system as I do not want to deal with hundreds of megabytes of non-free code. Call me pedantic, but I am a Debian developer after all. :)

Comment by madduck 07.13.06 @ 23:01h

Thanks for the Layout! Just a question: When I do it, it doesn’t display the “Incollection” category nicely. First, it gives me brackets around the years. Second, there’s a space missing after the period after the year. And there’s a space missing after the “eds.”.

Comment by Dominic 07.17.06 @ 19:57h

For my thesis I used Bibdesk (Mac Os X).. It also uses BibTex as a format. I espacielly liked the additional scripts.

Comment by daniel 07.19.06 @ 10:52h

Hi Matthias,
as a thank-you for the nice blog-post about JabRef here the OrgSci-LayoutFormatter:

package net.sf.jabref.export.layout.format;
import net.sf.jabref.AuthorList;
import net.sf.jabref.AuthorList.Author;
import net.sf.jabref.export.layout.LayoutFormatter;
public class AuthorOrgSci implements LayoutFormatter {
  public String format(String fieldText) {
    AuthorList a = AuthorList.getAuthorList(fieldText);
    if (a.size() == 0){
      return fieldText;
    }
    Author first = a.getAuthor(0);
    StringBuffer sb = new StringBuffer();
    sb.append(first.getLastFirst(true));
    for (int i = 1; i < a.size(); i++){
      sb.append(", ").append(a.getAuthor(i).getFirstLast(true));
    }
    return sb.toString().replaceAll(”\\. (.)\\.”, “\\.$1\\.”);
  }
}

Maybe you can convince me to add this to the next JabRef release… :-)

Comment by Christopher Oezbek 09.02.06 @ 12:59h

You may also check out another literature management software. It’s called synapsen and has many interesting features, special support for BiBTeX as well. You’ll find it here:
http://www.verzetteln.de/synapsen/

Comment by Antonia Brecht 09.18.06 @ 20:03h

i am new to jabref - i intend to use it for my postgrad practice led research in digital arts - i am try ing to find the standard export filters can you help

thanks

paul:-)

Comment by paul thompson 09.30.06 @ 23:00h

Have you try Bibus…

This project is just at his beginning but you can already insert, format and actualize you reference in openoffice easily…

On other hand… I use you new java class for better formating my reference, but I need to put a et between the last two authors… I would like tu edit your java class and change it a bit…

I try to edit the one that come with JabRef, but I have been unsuccessfull…

Do you have a idea of how should I edit java class?

Thanks a lot!

Comment by Guy 05.31.07 @ 16:10h

Hi I’m quite new to LateX and jabref and I have the following question:
I would like to write an article for the journal Polymer using LateX in my Latex file I use the \cite command to designate my references.
However I get then the following layout:
1. G. Kim, G. Michler, POLYMER 39(23)(1998)5689-5697
whereas the layout should be:

1. Kim GM, Michler GH. Polymer 1998;39(23):5689-5697.

How can I get the references layout changed automatically? Is this done using the customised export filter?
It would be greeat pf someone could help me.
Thanks a lot in advance,
Nico

Comment by Nico 06.18.07 @ 10:51h

I can recommend the following tool:
Zotero (http://www.zotero.org/)
You need a firefox 2.x. Installation is a snap and importing, tagging is really easy.
Give it a try.

Comment by Uwe Brahm 01.10.08 @ 15:11h

Hi, thanx for the Jabref filter :)

Comment by Elke 04.16.08 @ 18:47h

Hello, thanks for the OrganizationScience layout. I have modified this one to export in ACS fashion.

Comment by Emilio 05.03.08 @ 0:53h



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