Bibliographic Management meets Web 2.0

Regular readers of this blog know that I often talk about bibliographic management tools (most recently here and here), and it was probably for this reason that I was invited to an interesting full-day workshop last week at the Royal Free Hospital Medical Library in London: Bibliographic Management meets Web 2.0. The event was organized by science librarians Frank Norman, Nathalie Cornee and Betsy Anagnostelis, and was attended by about 20 science librarians. We had demos of the following software:

This is a fairly complete list of bibliographic software with Web 2.0 features. Missing are some tools with similar features, as there simply wasn't enough time and money to invite them all (e.g. 2collab and Labmeeting), several popular programs without these features (Reference Manager, Citavi and Papers), and JabRef and similar tools for BibTeX files used by LaTeX.

I gave a brief introduction of what features I would look for in a reference manager today (available on slideshare). The six presenters then took up a challenge (Word file here) that was given to them the week before. We used a simplified version of a set of tasks (find reference, put citation into Word document, etc.) originally developed for CiteFest at Northwestern University. Every participant was sitting in front of a computer and follow along with the tasks (the technical staff at the Royal Free did a marvelous job installing the software and bookmarklets on all computers before the workshop). The demos were nicely captured in the FriendFeed room we have set up for the workshop, so you can follow the details of the sessions there (the room also has some excellent links to other resources).

In the discussion at the end we all felt that all reference managers used that day were up to the challenge (Connotea and CiteULike couldn't put references into a Word document, but managed the rest of the tasks perfectly), and we decided not to declare a winner. We also felt that the market is developing so fast, that a feature comparison looked very different 12 months ago (e.g. Mendeley just launched, no Web version of Zotero), and will again look very different 12 months from today. Most librarians in the room therefore felt that they probably have to support most of these tools at their institutions. We briefly talked about the cost of these tools (of the tools that were demoed, only Endnoteweb and Refworks are commercial). This might be an issue when licenses have to be renewed. I've set up a reference manager feature comparison chart a few months ago, and have updated this chart after the workshop.

One feature I really like in Papers is fulltext search of the PDF files in your library, which I think is a much easier way to find information than tagging (and David Crotty agrees with me: Why article tagging doesn’t work). I was therefore happy to see that Zotero, Mendeley, CiteULike and Refworks all support this feature, something I have overlooked before. Fulltext search is one more reason that online reference managers should be able to store PDF files. Another reason is that several people working on the same reearch project shouldn't all have to go out and download the fulltext files themselves – or even worse, email them to each other. This sharing is not only an important features of Web 2.0 bibliographic tools, but is obviously also an area of potential problems with copyright (for papers that are not Open Access). CiteULike, Mendeley and Refworks all try to avoid these kinds of issues by allowing sharing of references and PDF files in private groups with a limited number of users.

It was interesting to see that the tools use very different approaches to integrate with the Web. Connotea, CiteUlike and Refworks are Web-based tools (the Refworks Write-N-Cite Windows module can download the reference database for read-only offline use), whereas Zotero, Mendeley and Endnote synchronize between a desktop version and web version. I'm really torn between these two approaches. Web-only reduces the cost of development and maintenance (no need to develop separate versions for Web/Windows/Mac/Linux, users don't have to install new versions). Desktop/Web allows offline use users always have a copy of their data on their computer. There is probably no right answer to this, email is another example where both approaches are very successful.

Only after the meeting did I realize another interesting difference between the various tools. They all have different business models behind them: Endnoteweb: (mostly) single-user licenses, Refworks: site licenses, Connotea: owned by a publisher, CiteUlike: independent with support from a publisher, Zotero: Open Source and Mendeley: Web 2.0 company that plans free and paid services. This might actually be a deciding factor in determining which of these tools will be the most successful in the long-term future.

But in the end, the similarities far outweight the differences between these tools. We didn't have time left to talk more about this, but for Bibliographic Management to move to Web 2.0, it's not really just about technology, but rather mostly about the users. We had an interesting discussion about that topic a few weeks ago (How to close the digital divide among scientists). I believe that ultimately your collection of references should sit in a database that is accessible from the web. Some references you want to share with everybody (e.g. via tools like FriendFeed), and that includes your own publications. And some references you want to share with private groups of people, e.g. people in your lab or when coauthoring a paper. All the tools presented in the workshop allow you to do that.

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19 Responses to Bibliographic Management meets Web 2.0

  1. AJ Cann says:

    Nice summary Martin, thanks for this from those of us who weren’t there.

  2. Rintze Zelle says:

    bq. “Zotero, Mendeley and Refworks all try to avoid these kinds of issues by allowing sharing of references and PDF files in private groups with a limited number of users.”
    Zotero currently doesn’t (yet) support file sharing in public or private groups. Users can only sync their personal files between computers if they have access to a WebDav service. (documentation: “”:
    I also wrote a “blog-post”: about Zotero yesterday, after finishing a draft of a research paper using Zotero, which touches on some things that also came up during the workshop.

  3. Martin Fenner says:

    Thanks AJ. There were of course a lot of small things that I didn’t mention. One example is bookmarklets, that all tools with the exception of Endnoteweb use. Not all bookmarklets can import several references at once (e.g. from the search results of a PubMed search), which would be a big time saver. Mendeley and Zotero allow you to do this, and CiteUlike “updated their bookmarklet”: with the same functionality one week after the workshop.
    Another related issue is the different approaches, that these tools use to search literature databases. Some of them search the databases (e.g. PubMed or Scopus) directly, and some use bookmarklets to import from the Web frontend to these databases. I would be interested to learn whether users prefer one approach over the other.
    Rintze, thanks for the great Zotero presentation. I’ve corrected the text above. And thanks for linking to you blog post. Text formatting in references is a big problem for many of these tools.

  4. Fergus Gallagher says:

    bq. “One feature I really like in Papers is fulltext search of the PDF files in your library … I was therefore happy to see that Zotero, Mendeley and Refworks all support this feature …”
    I’d like to point out that CiteULike also supports full text searching of PDF documents (Fergus@CiteULike)

  5. Martin Fenner says:

    Fergus, thanks, text is updated.

  6. Heather Etchevers says:

    Martin, I’m sure that we don’t as yet realize the full added value of your input and summary of the meeting here. Thank you for a tremendous amount of work.
    I also agree with one of your closing remarks that the business model may be a determining factor in which tool(s) persist over time. While I am happy with the open access or currently free tools that are available, I’m conscious that one very rarely gets something for nothing, and haven’t quite decided whether I would prefer site- or individual-specific licensing. The former, for sites that can play by the rules, enable young members of the scientific community to have access to these tools; on the other hand, inexpensive individual licenses, like WinZip proposes (or even less expensive for bona fide students), might be a good way to go as well.

  7. Martin Fenner says:

    Heather, I don’t think that it necessarily has to be individual or site licenses that pay for these products. It could also be publishers that want to provide these tools for free because they integrate with their other offerings (Connotea – Nature Publishing Group, CiteUlike – Springer, 2collab – Elsevier). Or you could provide the tool for free for up to 100 references (Citavi). Or you have a free basic service and pay for additional features, e.g. recommendations or detailed citation analysis (apparently this is what Mendeley plans to do). Or you distribute the cost of developing and distributing these tools to enough people that you don’t have to charge customers (Zotero). And what is a fair price for these tools? Endnote (new version or update) for many people is more expensive than Microsoft Office.

  8. Christina Pikas says:

    Yes – thank you for this great summary. I’m thinking about running a sort-of show and tell about these things at my place of work. One of our physical chemists mentioned Biblioscape ( I hadn’t heard of it before he mentioned it.
    As you know, I’m a real fan of RefWorks, but there is a real concern about if someone leaves an institution (they graduate or take another job) and moves to another without a subscription. University of Maryland didn’t renew their subscription this year – but they hadn’t marketed it heavily so there weren’t as many users who had to shuffle their stuff quickly. At least if you have a program loaded on your computer, you’ll still have it if the company goes away or you lose internet.

  9. Alex Holcombe says:

    BookEnds, although Mac only, is another good reference manager. Does what Endnote does I think, but is much less expensive

  10. Martin Fenner says:

    There is a “very long list”: of reference managers on Wikipedia. The lists gets much shorter (and then doesn’t include BookEnds) when you only look at the tools with Web 2.0 features.
    Christina, this is a valid concern. Refworks has an “Alumni Program”: for graduating students. And you can export all your references in a format like RIS that all reference managers understand.

  11. Martin Fenner says:

    I forgot to mention “Wizfolio”:, a Web 2.0 bibliography tool that launched last year and has most of the features (including a Microsoft Word plugin) that we have discussed here. Haven’t yet had a closer look, but there was a “FriendFeed discussion”: about it last year.

  12. David Crotty says:

    Always good to have an up-to-date list Martin, thanks. My question is what is going to happen to some of these services when a big corporation like MacMillan (who own the Nature Publishing Group) realize that they are set up to allow users to upload and redistribute MacMillan’s copyrighted material? I’m assuming that no lawsuits have been filed because there’s so little traffic on these sites, but if they catch on, don’t you think we’ll see the same sorts of legal maneuvers that shut down Napster?

  13. Martin Fenner says:

    David, you point out something important that you obviously “have also discussed with Victor Henning”: earlier this year. The different reference managers approach this differently. *EndnoteWeb* and *Connotea* simply are not allow uploading of PDF files. *Zotero* does allow syncing of your files, but does not allow sharing. *Mendeley* allows sharing in private groups of up to 10 people. *CiteULike* allows sharing in private groups of PDF files where the user has indicated that he owns the copyright of that file. The Refshare module of *Refworks* limits sharing to 1000 accesses per database per month.
    I would estimate that sharing of PDF files by scientists is often more about saving time (finding, downloading and storing references), rather than about copyright violations. If I organize a journal club in my department, write a paper with several coauthors from my institution, etc., everybody usually has the right to access the PDF file on an individual basis.
    A clever company would try to negotiate a clever deal between their reference manager and the journal publishers that would allow sensible sharing of references. This would probably require to also involve the research institutions, e.g. by allowing sharing of fulltext papers only from the same institution. And we shouldn’t forget that many papers from open access publishers and in institutional repositories can legally be shared.

  14. David Crotty says:

    There are some weak arguments about fair use being put forth by some of the reference manager companies, but from what I can tell, what they’re doing is pretty blatant infringement, particularly because users upload files to the company’s server and the company redistributes it. CiteULike appears to be trying to use the safe harbor defense and Mendeley seems to think that redistributing a file to ten people is somehow okay (but 11 would apparently be problematic). Haven’t spent much time with Refworks, so I can’t comment there.
    The good news is that I know some of these companies are negotiating with publishers, as there are ways that the two could work together and enhance each others’ products. It’s still an open question of whether these negotiations will go anywhere, whether lawsuits will win the day, and if any of the fair use defenses will hold up in court (so far, precedent doesn’t look good).
    That’s why I tend to advise people that if they’re going to use an online service, to think about using multiple services, and to regularly pull out a backup of your references from the online site, just in case the one you’re using disappears. Legal questions aside, this is probably best practice anyway, as a lot of these services are going to fall by the wayside.

  15. Frank Norman says:

    Martin – sorry to be late here. You very modestly omitted to say that you also provided a great deal of input to organising this event. Without you I am not sure it would have happened. I’d also like to thank Rintze Zelle for agreeing to come over from Delft and take us through Zotero’s features. All the products we featured had a UK representative who gave the presentation but Zotero did not so we nearly had to leave it out of the programme until Rintze agreed to help out.
    Re. business models, before the meeting I would, like Heather, have been concerned about the longterm prospects of free products. Steer clear unless you’re prepared to accept they were fragile, uncertain things. But the meeting made me realise that these days “free” does not equal “amateur, unstable”. OK, FriendFeed is perhaps an object lesson in what can happen, but takeovers also happen with commercial products (anyone remember ProCite?). All the products seem to have a great deal of stability and have big backers behind them.
    Leading on from that, an important issue is their degree of openness. I liked the fact that Mendeley and Cite-u-like cooperated so that you could import your Cite-u-like library into Mendeley (or was it the other way round?). This kind of inter-operability makes it less of a worry if one product is withdrawn – you can easily move your data elsewhere.
    Regarding the sharing of PDFs, I think that we will have to move on, just as the music world is, from expecting to rigidly enforce old-style copyright restrictions. As “Jim Griffin”: at UKSG last year “Copyright is not an enforceable business model. Publishers should run their affairs so that pirates are unnecessary”.

  16. Frank Norman says:

    p.s. Endnoteweb by the way is not just on single-user licences. Any institution with access to Web of Science (at least in the UK) also has access to Endnoteweb.

  17. Maxine Clarke says:

    I’m not in this particular loop as far as NPG is concerned, but just to note that NPG is always open to suggestions and comments re its licence to publish policies, particularly with respect to web 2.0 tools. We’ve been following the Zotero case and Nature has published an editorial in favour of what this service is aiming to do.

  18. Frank Norman says:

    Concerning the sustainability/mutability and open/closed issues, Bryan Kelly has an interesting “post”: on his blog today. He is writing about FriendFeed, but the issues are similar. He advocates a risk assessment as an aid to choosing which service is right for a particular user.
    One issue he highlights is that the community of users is important. As the BibMan products become “social” this aspect becomes more important. If, say geologists mostly use product X while particle physicists prefer product Y, then as a geologist you may prefer to to use product X because you will be interacting with your community more easily.

  19. Maxine Clarke says:

    You probably saw “this very positive Guardian tech blog piece”: about Mendeley.