Beyond My Mind

March 4, 2007

Comparison of Free Bibliographic Managers

Filed under: Research — mahbub @ 1:26 am

I never realized the scarcity of a good tool for managing personal bibliography database until recently. I was writing a paper and found that it is really difficult to manage hundreds of references and use them in a document. Beside my original research I started researching on this issue and found that no single tool can solve all the required tasks for this purpose. This post is a result of the search for a free tool that will best serve this purpose.

Here is how a bibliographic manager works. An author creates a document and cites his document with entries form a bibliographic database created earlier. After the author completed writing the paper he passes the document and the database through some application and the application incorporates all the references cited in the document from the database. This produces a final version of the document containing the text, graphics, etc. the author created along with the references he cited in a specific format. The entire process is shown in figure 1.

The bibliographic citation process

Figure 1: The bibliographic citation process

I will present a comparison matrix on all the available bibliographic managers. First I will decompose each bibliographic management requirements into several sub-objectives i.e. feature. Then I will present a table showing the supports for those features in available tools. However, I did not use all the bibliographic managers out there and it is not possible for a single person to use all of them. So I would request you to let me know about any tool you have used.

Expected Features in a Bibliographic Manager
There are six basic requirements expected from a bibliographic manager. Listed down below is a functional decomposing of these requirements.

  • Search: Search all the available academic/non-academic databases.
  • Store: Store the reference and possibly a soft copy of the reference.
    • Viewer: View soft copy (doc, pdf, etc.).
  • Annotate: Keep notes on the reference.
    • Overall: Just a single note on the reference
    • Anywhere: A note anywhere in the document
  • Communicate: Import from and export to different formats.
    • Import (BibTex, End Note, XML, etc.)
    • Export (BibTex, End Note, XML, etc.)
  • Platform: Run on different platforms (Linux, Windows, etc.)
  • Presentation: Present the data to some standard formats.
    • Formats (MLA, APA, etc.)
    • Document (doc, pdf, html, etc.)

Some Issues about Bibliographic Tools
The main hurdle in my opinion is to annotate the reference document. There are so many different and complex file formats out there that it is really difficult to add support for all of them. Also pdf, the mostly used format for file exchange is also very difficult to handle. There is no good free application or library to handle pdf. I know about pdf library iText and annotation tools like Jarnal and Multivalent, but even these are tough to incorporate into any system.

The next problem such software may face is to present the data according to some specific standard. There are so many different organizations and so many different formatting styles that it is really hard to add support for all of them. On the other hand some text processing systems, for example LaTeX, can produce a final document from a bibliographic database and source document, but others like Microsoft Word 2003 can not do it. Adding this support for all such systems is important but very difficult.

The platform issue limits the application to communicate between different systems.

The search capability has to deal with the differences in internet connection methods in different operating systems. Another issue is to provide search support for all different bibliographic databases in different research domains.

So it is easy to see why most of the free tools and many of the commercial tools do not support all the required functionalities.

Free Tools for Bibliographic Management
There are many different tools available for this purpose. They can be divided into three categories: Application, Web based, and Hybrid. A Google search on bibliographic tools returned this comprehensive survey on bibliographic tools. This list includes even the smallest possible script to count number of bibliographic entries in a database. The purpose of this writing is not to include every possible bibliographic tool but to compare the tools that are decent enough to do the tasks specified earlier. (update) Links to some other useful articles submitted by the readers:

Table 1: Comparison matrix on free bibliography management application.

AppType Tools Search Store Annotate Communicate Platform Presentation License*
Application JabRef Medline, citeseer, IEEExplore Pdf, ps Single note BibTex, RIS, MODS XML All HTML, RTF Open Source
Bibdesk** Pubmed, Z39.50 Yes Single note BibTex, RIS, MODS XML Mac HTML, RTF Open Source
PBib No No No BibTex, Endnote All HTML Open Source, Copyrighted
pybliographer Pubmed No No BibTex, Endnote All Unkn. GPL

HyperBIBTEX
Unkn. Unkn. Unkn. Unkn. Mac Unkn. Free, Copyrighted
KBibTeX Unkn. Unkn. Unkn. Unkn. Linux Unkn. GPL 2
Bibus yes no Single note RIS, Refer, Medline Windows, Linux, Mac Itegrates with Word and OOo GPL 2
Web based Aigaion Unkn. Yes Yes BibTex, RIS All HTML, RTF GPL
bibsonomy yes Unkn. Unkn. BibTex, RIS All Unkn. X
CiteULike yes Unkn. Unkn. Unkn. All Unkn. X
EasyBib yes Unkn. Unkn. Unkn. All Unkn. X
RefBase * yes yes Shared/ Personal BibTeX, RIS, MODS XML, COinS All ASCII, HTML, LaTeX, MarkDown, PDF, RTF, etc. X
BibConverter! yes no no IEEEXplr,
Eng Vil and
ISI.
All BibTex X
WIKINDX$$ PubMed yes yes BibTeX, Endnote, RIS All Rtf, HTML + format editor GPL
Hybrid Zotero yes yes Notes, Snapshots BibTex, RIS, MODS, RDF, Refer, Bibex, COinS All (firefox plugin) RTF, HTML# Open Source

This matrix is however, not complete and perfect. I hope to update it if I find more information. I would appreciate your feedback here.

Commercial Tools for Bibliographic Management
There are more applications than you can imagine for solving this problem. Norman listed almost all known commercial packages available in his website. He also has a Bibliographic Grid comparing almost all the commercial packages. This page, however, does not include Microsoft Word 2007. Microsoft recently added bibliographic support in Microsoft Word 2007. Although it is still in primitive stage, its conformance with open standard will allow people to come up with solutions in this area. This Microsoft Word 2007 team blog post on bibliographic feature will help you to know more about it. Also don’t forget to see this document in msdn2.

I could not find a single resource on free bibliographic tools when I was searching for it. Even the free bibliographic tools do not show up with a moderate Google search. After I found JabRef I promptly started using it. Later I found other tools. I have not used all of them. But the comparison matrix will definitely help me hunt down others and choose which one fits best for me. Hope this helps any avid researcher out there.

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100 Comments »

  1. great sharing!

    wish to see the update and ur final findings on the bibliography referral. i used google desktop to keep track of my research document and searching, and used that together with my manual process of referencing.

    cheers!

    Comment by Sadiq — March 4, 2007 @ 3:10 am | Reply

  2. It’d be useful to have the licenses listed, as some aren’t open source.

    refbase is a web-based app that:
    supports search
    supports storage
    has short note (either shared or personal) annotations
    can import/export BibTeX, RIS, MODS XML, and other formats
    Supports all platforms; has ASCII, HTML, LaTeX, MarkDown, PDF, and RTF

    Comment by atom prober — March 4, 2007 @ 11:02 pm | Reply

  3. Zotero can support multiple single notes and you can also associate multiple snapshots with a reference, given a unique comment on each one. It also supports MODS, RDF, and Refer/Bibix input/output & a few other formats. Both refbase and Zotero support COinS metadata.

    Comment by atom prober — March 4, 2007 @ 11:08 pm | Reply

  4. bibus is also worth a mention–it integrates with MS Word and OpenOffice.org Writer.

    Comment by atom prober — March 4, 2007 @ 11:13 pm | Reply

  5. More comprehensive lists of software are at Wikipedia and OpenOffice.org’s wiki

    Comment by atom prober — March 4, 2007 @ 11:17 pm | Reply

  6. Thank you very much atom prober. I hope to add the information you provided soon.

    Comment by mahbub — March 5, 2007 @ 12:11 am | Reply

  7. Interesting read. Your comparison matrix is very nice. I hope you’ll maintain and expand it.

    Some time ago I wrote a similar review of bibliographic managers. It mostly covers tools that work natively with BibTeX. You may also be interested in my online tool BibConverter, for easy conversion of bibliographic data from IEEEXplore, Engineering Village and ISI Web of Science.

    Comment by Kjell Magne Fauske — March 5, 2007 @ 2:57 am | Reply

  8. Building a comprehensive list of bibliographic applications and comparing all their features is quite a task, since there are many of them. The links given by atom prober give an idea how diverse the field of bibliographic apps actually is. Adding to the above links, more listings of bibliographic applications are given here:
    Open standards and software for bibliographies and cataloging
    List of bibliographic web applications

    Comment by Matthias — March 5, 2007 @ 11:08 am | Reply

  9. Thanks to Kjell and Matthias for you input. You are right Matt, it IS a diverse field. IMHO the reason is the complexity to perform the listed tasks.

    I will update the page tonight.

    Comment by mahbub — March 5, 2007 @ 11:14 am | Reply

  10. Zotero supports APA, Chicago style, MLA, and exports to RTF and HTML. (see http://www.zotero.org/documentation/frequently_asked_questions#how_do_i_create_a_bibliography)

    Comment by Richard — March 7, 2007 @ 5:46 am | Reply

  11. Updated. Thanks.

    Comment by mahbub — March 8, 2007 @ 1:12 am | Reply

  12. Comparison of reference management software on Wikipedia

    Comment by atom prober — March 8, 2007 @ 7:51 pm | Reply

  13. The comparison of reference management software on Wikipedia might be an effective way to collaborate on a more extensive comparison (though, due to notability concerns on WP, there are some products which shouldn’t necessarily migrate from your tables to the WP tables).

    Comment by atom prober — March 8, 2007 @ 11:55 pm | Reply

  14. WIKINDX (http://wikindx.sourceforge.net) is a free, GPL web-based application that:

    Imports/exports BibTeX, Endnote, RIS and has plug-ins to handle PubMed.
    Exports bibliographic lists to RTF or HTML.
    Supports user groups and user bibliographies.
    Unlimited and searchable quotes, paraphrases, notes etc.
    Unlimited attachments.
    Comprehensive search and select criteria.
    Comes with several bibliographic/citation styles (APA, Chicago, Harvard, IEEE etc.) and includes a web-based citation style editor to create/edit your own styles.
    Integrated WYSIWYG word processor allowing importation of quotes etc. and automatic citation formatting/bibliography appending when exporting the paper to RTF.
    A variety of translation/localization plug-in modules.
    The plug-in architecture allows for the easy writing of third-party modules.

    Used by NASA! ;)

    Mark

    Comment by Mark Grimshaw — March 9, 2007 @ 5:41 am | Reply

  15. […] bit with Derek Baird and reading his blog post from today about it. Derek also has published a nice “Comparison of Free Bibliographic Managers” worth checking out. He reviewed 14 different FREE tools for managing research citations! The […]

    Pingback by Moving at the Speed of Creativity » Blog Archive » More research tools — March 12, 2007 @ 8:12 pm | Reply

  16. […] Comparison of Free Bibliographic Managers « Beyond My Mind It is really difficult to manage hundreds of references and use them in a document. Beside my original research I started researching on this issue and found that no single tool can solve all the required tasks for this purpose. This post is a result of t […]

    Pingback by Internet (Web2.0) et ophtalmologie » links for 2007-03-18 — March 18, 2007 @ 3:20 pm | Reply

  17. […] Filed under: Research — mahbub @ 1:23 am Inspired from the responses of my post comparing free bibliographic tools, I planned on posting few more articles about different research tools. Here I am presenting a […]

    Pingback by Comparison of Bibliographic Search Engines « Beyond My Mind — March 19, 2007 @ 1:23 am | Reply

  18. Hi everybody! :)

    I used to work with Latex and Jabref for manage my thesis stuff, but for “external reasons”(*) now I had to migrate everything to Word 2007, therefore I supossed that Endnote X is a good choice (any suggestions??).

    But, I don’t have any clue for how use Endnote X within Word 2007 :(

    Or in the other hand, how can I convert from Endnote file format to Microsoft Word 2007 bibligraphic source (XML based)???

    Obviously re-write my references is not a choice.


    (*) research group motivation, and lack of more persuasive arguments from my side… :(

    Comment by Francisca R. — March 24, 2007 @ 8:35 pm | Reply

  19. sorry, after all I had to read this link:

    http://www.endnote.com/support/faqs/cwyw/faq43.asp
    ;)

    Comment by Francisca R. — March 24, 2007 @ 9:04 pm | Reply

  20. Hi Francisca,
    We are writing an export module for JabRef. Thanks for letting us know.

    http://mahbub.wordpress.com/2007/03/22/deciphering-microsoft-office-2007-bibliography-format/

    Comment by S M Mahbub Murshed — March 24, 2007 @ 11:16 pm | Reply

  21. Francisca, if you can (or want) to use the native Word 2007 bibliographic feature instead, you could also try to use Bibutils which has recently added support for conversion of EndNote XML files to Word 2007 bibliography XML format:

    http://www.scripps.edu/~cdputnam/software/bibutils/

    Comment by Matthias — March 26, 2007 @ 5:19 am | Reply

  22. BibDesk additions:
    Search: Z39.50
    Store: Any document
    Annotate: Single note
    Presentation: HTML, RTF

    Comment by AHM — March 26, 2007 @ 11:30 am | Reply

  23. […] of bibliography software Beyond My Mind has a list of what is currently available, and a comparison table. This list is useful especially […]

    Pingback by academhack » Blog Archive » More Useful Stuff Elsewhere — March 28, 2007 @ 8:00 pm | Reply

  24. Thanks AHM. I included your input.

    Comment by mahbub — March 30, 2007 @ 1:40 am | Reply

  25. Another open-source Java application, hardly mentioned anywhere

    http://www.itp.uni-hannover.de/~saemann/celsius.html

    Comment by dalai — June 21, 2007 @ 8:25 am | Reply

  26. I am in search of a better solution to my plans to enrich my project: http://www.anable.com/MONSON/index.html
    with links to other sites and services as found on search engines such as Google, but I don’t like the idea cutting & pasting the occasional relevant hit into my local XML table, and then integrating it into the appropriate webpage as well as generating a comprehensive list/table on another webpage.

    Do you have any suggestions or ideas?

    PS: I was a systems librarian who made some modest contributions to the LC MARC-S developments in the 1970s.

    Comment by Richard Anable — July 11, 2007 @ 11:40 am | Reply

  27. Keep it up.. nice site for ref. Sri Lanka

    Comment by Supun — August 22, 2007 @ 11:05 pm | Reply

  28. […] mahbub.wordpress.com/2007/03/04/comparison-of-free-bibliographic-managers […]

    Pingback by new world order — October 22, 2007 @ 8:12 am | Reply

  29. […] Useful table highlighting the features of various free bibliographic managing tools. […]

    Pingback by Blogging IT and EDucation » Blog Archive » Comparison of Free Bibliographic Managers — October 24, 2007 @ 8:51 am | Reply

  30. […] Useful table highlighting the features of various free bibliographic managing tools. […]

    Pingback by PhD » Blog Archive » Free bibliographic Managers. — October 24, 2007 @ 10:56 am | Reply

  31. Excelent analysis. JabRef works perfectly for me.

    Comment by ponzonha — October 29, 2007 @ 5:11 am | Reply

  32. Many articles on the internet provide instructions for citing the article and given options such as APA, MLA, … The ironic thing about this article on citations is that it doesn’t give any citation information – not even the name of the author. How should I cite this information?

    Comment by graham — November 10, 2007 @ 7:37 am | Reply

  33. Follow these guidelines and you will build that new home with little, or no, problems. atlanta bathroom remodeling can help…

    Comment by nemnweennaLar — November 19, 2007 @ 1:49 am | Reply

  34. which program would you recommend for accomplishing the following:

    searching pubmed, and then sorting the information by author so that I could know quickly and efficiently how many articles each author had written, how many review articles each author had written, etc.

    Thanks so much

    Comment by lee tilson — November 23, 2007 @ 3:11 pm | Reply

  35. […] Comparison of Free Bibliographic Managers […]

    Pingback by Manage References with JabRef « Entangled — December 10, 2007 @ 2:19 am | Reply

  36. Even though BibDesk itself only supports a single note, it integrates well with Skim, a Mac OS X only PDF viewer with advanced annotation features. BibDesk then collates the Skim notes and shows them in the database.

    I just wish BibDesk was easier to use with MS Word, since many of my collaborators only use Word.

    Comment by Janssen — August 26, 2008 @ 10:07 am | Reply

  37. […] Comparison of free bibliographic managers […]

    Pingback by Personal bibliographic management software | Ionut's WebSpace — October 4, 2008 @ 4:53 am | Reply

  38. […] public links >> wikindx Comparison of Free Bibliographic Managers Saved by Osmosis on Sun 02-11-2008 Moodle has 12 SoC developers Saved by Satoshigirl on Sat […]

    Pingback by Recent Links Tagged With "wikindx" - JabberTags — November 2, 2008 @ 11:04 pm | Reply

  39. […] both Open Source (JabRef, pybibliographer) and commercial (EndNote, RefWorks etc). See here and here for comparisons between various […]

    Pingback by BibDesk and Word « So much to do, so little time — November 19, 2008 @ 11:20 pm | Reply

  40. I have been using JabRef for about 4 weeks now and I find it very useful in managing my references and related pdfs. I have been using it for writing my PhD dissertation and I wonder what I would have done without it. Within weeks I have been able to add over 350 references with abstracts and pdfs, where available.

    Making citations in Word 2003 has been possible through the BibTeX2Word template provided by Mike Brookes. Generating references in a vast range of styles is now possible. Since I use the MikTeX package as the TeX/LateX engine which also incorporates the BibTeX engine, I am able to download style files as and when I need them.

    The only difficulty I’ve had with JabRef is in exporting but I have to confess I’ve been too busy to learn the intricacies of the export creation task. Maybe, when I have some time I will learn this too. Import is relatively simpler in JabRef. But, overall, JabRef has been highly satisfying to work with.

    Strongly recommended for those who like to use freely available open-source software and are willing to experiment a bit.

    Shashank

    Comment by Shashank — April 13, 2009 @ 12:17 am | Reply

  41. Oh, about JabRef — I forgot to mention one important bit of feedback that I couldn’t get JabRef version 2.4.2 to work with MySQL, despite following the instructions provided. This would have been very useful, as then I would be able to maintain all my references in a great database. Hopefully, I will
    get this feature working when I get some spare time or someone else will solve this problem in the open source community.

    Shashank

    Comment by Shashank — April 13, 2009 @ 12:25 am | Reply

  42. Mahbub, that’s a great list! Recently, a new tool called Mendeley got a great writeup in Techcrunch, so you may want to add Mendeley to your list.

    Comment by Mr. Gunn — May 12, 2009 @ 1:37 pm | Reply

  43. Zotero is my opinion is the best. You can also look into a competing Web 2. based bibliographic manager called WizFolio (https://www.wizfolio.com/Default.aspx). But this one , though free, is not an open source program.

    Comment by Rijo — July 29, 2009 @ 8:35 am | Reply

  44. I was writing my research paper and using Endnote X3 trial version, I was worried what will happen to my project after trial expiry as Endnote is beyond my budget. Thanks to you I have been introduced to Zotero, completely match my requirement.

    Comment by Dr. Ashfaq Ahmed Bhutto — October 25, 2009 @ 12:45 pm | Reply

  45. I have now upgraded to JabRef version 2.6Beta and have to report that export to a MySQL now works perfectly. Besides JabRef I have also used Mendeley. Data excange between JabRef and Mendeley has been absolutely seamless. Mendeley has a useful feature that you can maintain your bibliographic databases on your PC desktop as well as on a web-site and periodically synchronize them whenever you want to. This way you have access to your bibliography wherever you happen to be. I have also used Bibliographix which happens to be an excellent tool at a relatively low cost of Euro 49 for an student licence. I use JabRef, Mendeley and Bibliographix quite interchangeably.

    Comment by Shashank — October 25, 2009 @ 8:27 pm | Reply

  46. For users of Word 2007, check out handycite at fks-soft.com. It is a freeware.

    Comment by Muhammad Suri — November 4, 2009 @ 5:58 am | Reply

  47. Any portable apps out there that would manage references as the above programs?

    Comment by kim — November 10, 2009 @ 11:49 pm | Reply

    • Zotero is portable by all means. Because this is only a firefox extension. Wherever u have internet connection and firefox zotero will work.

      Comment by Rijo — December 19, 2009 @ 11:30 am | Reply

  48. kim – I believe Papers has a iphone app for Mac users and Mendeley is developing a cross-platform mobile interface as well.

    Comment by Mr. Gunn — November 11, 2009 @ 11:00 am | Reply

  49. Check out BiblioExpress:

    http://www.biblioscape.com/biblioexpress.htm

    Comment by Oxa — December 19, 2009 @ 10:57 am | Reply

  50. […] and as a doctoral student at the University of Rochester I came to experience the powerful online research and bibliography tools available.  These tools stored my research in the cloud and enabled me to work on my dissertation […]

    Pingback by Q. How many index cards does it take to write a paper?……A. 1 URL | ISC's Blog — September 23, 2010 @ 5:24 am | Reply

  51. Hi there.

    You may want to include Qiqqa on your list, which has some interesting features related to all this.

    Thanks.

    Comment by Nik — August 13, 2011 @ 5:44 am | Reply

  52. My first post! :)

    Comment by Zvezdoros — September 30, 2011 @ 1:52 am | Reply

  53. […] trying them I ended up purchasing a student edition of EndNote because it is so much better.  Here is a list of free bibliography and reference managers. Or you can check out the wikipedia page which compares all reference managers, free and […]

    Pingback by The Best Free Software for Students | ShortWhiteCoats.com — November 13, 2011 @ 5:07 pm | Reply

  54. Easybib.com is by far the best.

    Comment by Ryan — May 30, 2012 @ 2:32 pm | Reply

  55. Question: I would like to get a free service that stores and cites (mostly psychology) articles. I have a mac and I am am especially interested in citing APA style in microsoft office and also I would really like to be able to browse abstracts. Can you recommend a free service that meets those needs?
    Thanks in advance!

    Comment by Lacey — July 10, 2012 @ 1:39 pm | Reply

    • Hi Lacey,

      May I suggest Mendeley? http://mendeley.com Happy to help you get started if you need.

      Comment by drgunn — July 13, 2012 @ 9:07 am | Reply

      • Thank you Dr. Gunn. I just downloaded the trial version of endnote and I am thinking of also downloading Mendeley to compare the two. If you are familiar with both do you perhaps know of any significant differences between the two (aside from cost)?

        Best,
        Lacey

        Comment by Lacey — July 13, 2012 @ 10:08 am

      • Also, do you work for Mendelson or are you an academic user?

        Comment by Lacey — July 13, 2012 @ 10:13 am

      • I downloaded both and so far I like Mendeley best! Thank you for your rec. I also noticed you in the video so I assume you work for Mendeley. May I ask how to edit a document once it has been imported? For example, many of the articles were automatically entered but some of them are only entered via the title I gave them when I saved them.

        Comment by Lacey — July 17, 2012 @ 8:36 am

      • Hi Lacey,

        To edit an entry, just select it and click in the field you wish to edit in the details view. Details are automatically retrieved for most papers which have an identifier such as a DOI and for the rest, we extract the details from the paper itself, not from the file name.

        The “needs review” folder shows the papers which we’re not sure we’ve got correct details on.

        Comment by drgunn — July 17, 2012 @ 9:14 am

  56. Fabulous, thanks!

    Comment by Lacey — July 17, 2012 @ 9:51 am | Reply

    • Dear Dr. Gunn,

      Oh dear, I can’t get the insert citation toolbar to appear… I have a mac with Windows 2008. The toolbar is very minimal and I have no idea how to cite in word… I downloaded the tool and followed the instructions provided on p. 10 of the manual but alas it is to no avail.

      Any suggestions?

      Best,
      Lacey

      Comment by Lacey — July 17, 2012 @ 11:28 am | Reply

      • Lacey,

        Send an email to support@mendeley.com and we’ll get you sorted out. Please describe the problem as best you can can, from the start, because the person reading the message won’t be me.

        Comment by drgunn — July 17, 2012 @ 11:32 am

  57. Thank you for you efforts in pulling this together for us. Your experience is very helpful.

    I’m debating between http://www.zotero.org/ and http://jabref.sourceforge.net/ for use with VUE (Visual Understanding Environment) and / or SciPlore.

    What is your experience with integrating visual concept mapping tools?

    Comment by teachjim — December 27, 2012 @ 11:06 am | Reply

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