Reference Manager Overview

18 April 2009: I've updated the chart and added 2collab, the “Read” category, sharing of PDF files and the Mendeley bookmarklet and fulltext search.

15 July 2009: I've updated the chart to indicate that Mendeley and labmeeting have integrated PDF viewers, and that 2collab can search Scopus.

20 July 2009: I've added the offline version of RefWorks for Windows, EndNote OpenOffice plugin and fulltext search in several tools.

22 February 2010: Many small changes, including a few more categories. Added Citavi and dropped 2collab, LabMeeting and Connotea.

6 August 2010: Added Mendeley API and iPhone app, EndNote X4 features.

19 September 2010: Moved chart to different location, PDF download, Creative Commons license.

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24 Responses to Reference Manager Overview

  1. Ricardo Vidal says:

    Hey Martin, that looks great. I was putting something similar together but I guess I can stop where it’s at. Nice work.

  2. Martin Fenner says:

    Thanks Ricardo. And congratulations for becoming the first Mendeley “community liaison”:http://my.biotechlife.net/2009/03/04/community-liaison-mendeley/.

  3. Pedro Matos says:

    Great summary of what to expect from these services! I wasn’t aware of the latest features in zotero beta but it looks promising. Currently I’m not relying on any specific service to handle all my article library. Just using CiteULike for some bookmarking and waiting Mendeley to mature a little bit (Windows user).
    Hoping to see more and more colored squares in that table soon!

  4. Martin Fenner says:

    Pedro, the “new sharing and syncronisation features”:http://network.nature.com/people/mfenner/blog/2009/03/04/zotero-interview-with-trevor-owens really make Zotero a much more interesting application. But Conntea and CiteULike still have much more polished social features.
    I also use more than one service. It is possible that we will have a service that covers everything in the future. But a better integration of these services through an API (and not just import/export of RIS or BibTex files) is the much better solution. The “announcement of a Mendeley / CiteULike collaboration”:http://www.mendeley.com/blog/2009/02/citeulike-and-mendeley-collaborate/ is a step in the right direction.

  5. David Crotty says:

    One category you might want to add–full text search of the papers themselves, something I find more valuable than many of the other activities listed. You also might want to differentiate between the services that let you store lists of papers and links online with those that allow actual uploads of pdf’s.

  6. Martin Fenner says:

    David, somehow I’m not surprised that you prefer full-text search over tagging (after reading your recent post “why article tagging doesn’t work”:http://www.cshblogs.org/cshprotocols/2009/02/23/why-article-tagging-doesnt-work/), but you are right. Another important feature that I didn’t list is the automatic extraction of reference information (metadata) from one or more PDF files on your hard drive – Papers and Mendeley are pretty good at this.
    There are big differences in how the features listed are implemented (e.g. storing of PDF files or just the reference). I will have to add a second page with a table that explains the various services in more detail (with columns: summary, good, not so good, ideal user, price).

  7. William Gunn says:

    Martin, you could also put a red square in the Mendeley column for bookmarklet, since they’ve got that now. The search and metadata extraction would also be awesome rows to add to the chart.

  8. Martin Fenner says:

    William and David, I followed your suggestions and updated the chart. I’ve also added 2collab. The new “Read” category explains why I love Papers. It’s built around PDF files, while most other reference managers just link to the PDF file on your hard drive. Sharing of PDF files is for the next version.

  9. William Gunn says:

    That looks great, Martin! “Mendeley”:http://www.mendeley.com/blog/2009/04/mendeley-desktop-v064-beta-coming-soon-work-on-v070-started-already/ 0.7 is coming soon, and will also have the integrated PDF viewer, to support collaborative annotation and sharing of notes.

  10. Martin Fenner says:

    Thanks William. I’m sure I will update the overview again in the future. I already had to fix a small mistake that I introduced into version 1.2 of the chart: Endnote works closely with Web of Science (both are Thomson Reuter products) and not Scopus (Elsevier). Scopus in turn integrates with 2collab (Elsevier), but also RefWorks (a ProQuest product). Connotea is from the Nature Publishing Group, CiteULike is sponsored by Springer. Mendeley, Papers and LabMeeting are made by Web 2.0 startups. Zotero and JabRef are Open Source products (the source code is also available for Connotea). Endnote, RefWorks and Papers cost money, all the other reference managers in the list are free to use. A future version of the chart should look at the price, business model and sustainability of these services.

  11. David Caplan says:

    Labmeeting actually does metadata extraction when uploading PDFs. It also provides an in-browser PDF viewer and supports full text search of the PDFs that you have uploaded.

  12. Martin Fenner says:

    Thanks David. But as I understand it, the fulltext PDF search doesn’t work across your PDF collection. I will update the chart accordingly.

  13. William Gunn says:

    Hey Martin! Since this chart has been so useful to point people to over the past couple months, would you mind updating it for the recent release of “Mendeley”:http://mendeley.com , which is now at the 0.9 version.
    The new features are the integrated PDF viewer in the Read category and OO and BibTeX compatibility in the Write category.
    Thanks again, it’s been real useful to have this chart to point people to.

  14. Martin Fenner says:

    William, I’ve updated the chart accordingly.

  15. William Gunn says:

    Cheers!

  16. Sebastian Karcher says:

    Martin: nice overview.
    AFAIK, there is no Endnote version for Linux.
    Zotero by now also has a retrieve metadata function – it appears to work slightly better in Mendeley and Papers, but it’s pretty good and improving in Zotero.
    Also, personally I don’t think the Mendeley export to BibTex feature is actual LaTeX writing support, but if that’s your bar, my understanding is that Zotero (and I believe even endnote) have the same capability.
    On the pdf viewer – what’s the criterium there? Zotero can open files with the adobe (or any other) plugin for FF, for me that’s within the program – you don’t have to leave Zotero to see the pdf. The breakthrough feature really would be annotation on pdfs and none of the programs has been able to solve that one yet. Papers is probably closest, because they don’t need cross-platform solutions.

  17. William Gunn says:

    Sebastian – Mendeley has a built in PDF viewer which supports sharable annotations. It works pretty well in the latest release, too.

  18. Sebastian Karcher says:

    thanks for updating – as per my comment above, I still don’t understand why Zotero isn’t supposed to have a function to extract metadata for pdfs:
    http://www.zotero.org/support/retrieve_pdf_metadata
    also, I don’t understand what type of LaTeX support Mendeley offers that Zotero doesn’t – if anything, Zotero, through the Lyz plugin
    http://www.klubko.net/?page_id=945
    has tighter BibTex integration.

  19. Sebastian Karcher says:

    also, Zotero has a SCOPUS translator
    http://www.zotero.org/translators

  20. Hans Siem Schweiger says:

    Thanks for this overview, it’s quite instructive. But I’m sure that Citavi also supports OOWriter and LaTeX – just change the cross-project options (choose Writer for standard word processor and tick TeX support). And an English version is on the way!

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  22. Unknown Unknown says:

    Hi Martin,
    Great comparison chart! Thanks for compiling this list.
    I was hoping you could please add Qiqqa to the list (http://www.qiqqa.com). It supports the following features:
    Search: None (although it does have a built in browser that is similar to Bookmarklet)
    Share: WWW, PDF files (sync)
    Store: Windows
    Read: Extract metadata, fulltext search (with OCR), PDF viewer
    Write: LaTex
    You might also want to update Mendeley’s column: they now have API.
    Have a great weekend!
    Jimme (jimme@qiqqa.com)

  23. Adele van der Merwe says:

    RefWorks works well in OpenOffice but Write-N-Cite is not compatible. Hoewever, it is very easy to get use to using the switches with the Ref Id. Thank you for this comparison – it is going to make things easier for me and also introduced me to two new products that I wasn’t familiar with.

  24. Martin Fenner says:

     Adele, thanks for the feedback. In the chart I list word processors that work with the plugin, therefore RefWorks is not listed for OpenOffice.