Dream & Passion: Finding the right bibliographic/reference tool

From: http://www.fauskes.net/nb/bibtools/

Handling references and bibliographic information is an essential part of all research. Summarized, this task can be divided into three parts:

Finding
Organizing
Displaying/formatting

As a PhD student, I need tools to help me with these tasks. In this article I will share with you some thoughts and experiences I have had during my search for the right bibliographic tool.

Update: Added Referencer to the list of tools.

Update: Added RRiki to the list of tools.

Update: Added KBibTeX to the list of tools.

What I am looking for

Finding references has become quite easy. Services likeEngineering Village , IEEE Xplorer and many others make it a breeze to search huge online bibliographic databases. Thousands of reference records and full-text articles are available for download, making it easy to have your own personal library stored on your hard disk. A good bibliographic tool should make it easy to import and organize downloaded references and documents.

When it comes to formatting bibliographic information in articles and reports, there is for me only one option:BibTeX and LaTeX. BibTeX uses style files to produce bibliographies, and handles all the formatting. Some bibliographic tools come with hundreds of output styles for different publications. For me this is not important, since I let BibTeX do all the work.

Many people use MS Word, even though Word is not well suited for writing scientific papers and technical reports. Most of the commercial bibliographic software can easily be integrated with MS Word. However, for me it is more important to have BibTeX support than a nifty Word plug-in.

So what I am looking for in a bibliographic tool is:

Easy to import references from online sources.
Must support common bibliographic formats, especially BibTeX.
It should be possible to organize references in categories, by authors, by keywords etc.
Nice and functional GUI
Non-hassle interface with BibTeX and LaTeX.
Easy access to electronic documents and URLs.
MS Windows compatible. Cross platform is a plus
Should not cost me a lot of money :-)

The tools

A quick search on the Internet reveals that there are many tools to choose from. Fortunately there exist a few web pages that have links to and describes most of them. Two such pages are:

The latter covers only free and open source tools.

Commercial software

The most popular commercial tools seem to be:

All three are from Thomson ResearchSoft. They have a long history and are recommended by many universities . Their user interface seems to be unchanged since the Windows 3.1 era, and would have benefited from a face lift. They are all quite similar in functionality and have tons of import/export filters and output styles. ProCite also has some nice functionality for organizing references in groups.

Some tools with more modern user interfaces are:

The first three programs on the list have much of the same functionality as the software from Thomson. Biblioscape and Bibliographix have built in word processors that let you write notes and drafts. They also offer functionality for organizing references in folders. BibTeXMng is a shareware program for manipulating BibTeX files.

If you do not need software that runs on your personal computer, there exist tools that only need a browser and a connection to the Internet. Two such tools are:

Free and open source software

I have always been attracted to free and open source software. I have no principles against commercial software, but when I compare free and commercial software in cost-benefit terms, free and open source software tends to win.

Among the free software are most of the tools that use the BibTeX format as their native database or output format:

BibEdit: A small and simple program for creating and editing BibTeX files. No import or export functionality. Windows only.
BibDB: A BibTeX database manager, bundled with Scientific Workplace. Has an ancient looking GUI, but has a decent set of features.
JabRef: A Java based graphical front end to manage BibTeX databases. Nice GUI, can easily import from online sources and is actively developed.
Pybliographer: A framework for managing bibliographic databases. Written in Python. Provides a scripting environment and a Gnome GUI. Can also be used with formats other than BibTeX.
BibDesk: Graphical BibTeX-bibliography manager for Mac OS X.
KBibTeX: A graphical BibTeX editor for KDE.
Referencer: A Gnome application for organizing documents and references. Supports automatic meta data retrieval if aDOI code or ArXiV ID is available.

My favourite is currently JabRef. It is an excellent program. The group functionality in JabRef has improved a lot in the latest versions and is now quite powerful. The import-filters are not perfect, but JabRef is constantly evolving and they will probably be improved in future versions.

I am attracted to Pybliographer since it is written in Python, my favourite programming language. Sadly the GUI only runs on Linux, and it does not have all the features of JabRef.

All of the tools above are basically front ends for plain BibTeX files. I find this very convenient and it's a good solution for single users. However, if a bibliographic database is to be used and edited by multiple users, it may be a problem to keep everything in a single BibTeX file. A solution to this problem may be to have an online bibliographic database with a web front end. Some such tools are:

WIKINDX: A web based bibliographic and quotations/notes management and article authoring system designed either for single use or multi-user collaborative use across the Internet.
refbase: A web-based, platform-independent, multi-user interface for managing scientific literature and citations
Aigaion: A web-based platform for managing annotated bibliographies. It allows the user(s) to order publications in a self-chosen topic structure

All of the tools run on the Apache web server with PHP and MySQL. They have good support for BibTeX, but they also support other bibliographic formats compatible with Endnote, Refman, Procite etc. The main strength of a web based tool is that multiple users can use and maintain a common bibliographic database. Personally, I find web applications a bit awkward to use compared to desktop applications. However, with technologies like AJAX, web applications will become more attractive.

RRiki is an interesting mix between a desktop application and a web application:

RRiki: A tool for storing and organizing information on citations for sources (articles,books etc), notes, figures and dossiers on researchers. RRiki uses the Ruby-On-Rails framework to display and store information on a MySQL database via a web-browser.

For information about other free tools, take a look at theOpen standards and software for bibliographies and cataloging page.

Concluding remarks

I am currently using JabRef for organizing my bibliographic information. It satisfies many of my needs. Some of the commercial alternatives may have more features, but most of them are too MS Word oriented and lack proper BibTeX support. I am also reluctant to pay for software when the free alternatives are so good.

The web based tools are very interesting alternatives, but with my current work flow I prefer to work directly with the BibTeX files. However, I see the usefulness of having an online bibliographic database and I will probably create one in the near future in addition to my personal BibTeX database.

I still haven't found the perfect bibliographic tool. However, by choosing open source tools I can contribute to and influence the development. My first contribution isBibConverter, a simple web-application that converts citations from IEEEXplore, Engineering Village and ISI Web of Science to the BibTeX format. The tool outputs BibTeX records that are more accurate and contains more information than when using the export functionality of IEEEXplore and EV2. Read more about BibConverter in a separate notebook entry.

Saturday, May 16, 2009

Finding the right bibliographic/reference tool