What is a reference manager?

Next month I will participate in the Innovations in Reference Management event organized by Owen Stevens from the Open University. My own presentation has the title Trends in Reference Management, where I will try to focus on three emerging areas:

  • Use of mobile devices for reference management (e.g. Nature.com iPhone App, Papers for iPad, Scopus Alerts for iPhone)
  • Social networks as discovery tools (using CiteULike, Twitter, FriendFeed, ResearchBlogging.org, etc. for finding relevant references instead of keyword searches in databases)
  • Integration of unique author identifiers (specifically ORCID) into reference management tools. This will allow many interesting uses of reference lists (e.g. for automated researcher profiles or evaluation)

Reference management has obviously come a long way from the desktop applications created 25 years ago. In 2010 it is difficult to give a good description of the typical functions of reference managers. My 8 answers are below.


At their core all reference managers are databases that store references. They should allow the user to create or import all required reference types, find duplicate records, and connect references by the same author or published in the same journal. I don't think any reference manager completely supports even this small feature set (most of them don't do author disambiguation). And we rarely use reference managers in a much broader sense, e.g. for storing important blog posts or references to research datasets (as suggested by Cameron Neylon).


Reference managers should put references into manuscripts, allowing a variety of citation styles. Only a few reference managers allow the user to edit citation styles, an important feature if an obscure style is required. Surprisingly, the functionality for reference management is usually not built into most word processors, but rather provided by the reference management software.


All reference managers can import references directly from bibliographic databases, either by direct database connections, or via bookmarklets.


Some reference managers (most notably Papers) not only manage references, but also organize the fulltext PDF files associated with them. There are many good reasons to keep the assets (such as scientific papers) and their metadata (the references) connected, e.g. to allow fulltext searches in your reference manager. Scientific journals have started to embed reference metadata in fulltext PDF files (XMP Labelling for Nature), making it easier to connect reference and PDF file.


Many reference managers now offer a web-based version. This allows using the same reference database with more than one computer and sharing of references with others. Some reference managers (e.g. CiteULike, RefWorks) only provide a web-based version.


Many bibliographic databases (e.g. PubMed or Scopus) now allow user accounts with storing of search strategies, interesting references, etc. Does that make them reference managers?


The flow of reference information has become much more complicated than simply from online database to reference manager to manuscript. Institutional bibliographies are a good example.


More and more we find interesting references not via keyword searches in databases, but rather through our social networks. This could be via CiteULike recommendations, blog posts discussing a paper on ResearchBlogging.org, or one of your contacts talking about an interesting paper on Twitter, FriendFeed or Facebook. Current reference managers don't provide good functionality to handle this user behavior.

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16 Responses to What is a reference manager?

  1. William Gunn says:

    Thanks for the nice overview, Martin. Of course, I might argue that Mendeley is more notable for PDF organization, if only because Mendeley works on almost all operating systems, whereas Papers works only on the Mac and thus only addresses a minority fraction of computing market share.
    I’m sure you knew I’d pipe in to say that, though 😉 Papers is a fine program and notable in its own right.

  2. William Gunn says:

    Just to be clear, Martin would have known I’d pipe in on this because Mendeley is a client.

  3. steffi suhr says:

    Thanks for this overview Martin! Very helpful and timely for me 😉

  4. Duncan Hull says:

    Hi Martin, this is a useful summary, its more complicated than it first looks…. I wondered where you see Mendeley fitting in to your classification?

  5. Unknown Unknown says:

    Hi Martin,
    Thanks for this overview! There are some great ideas in there.
    While doing my PhD I have come across several shortcomings with the existing reference managers. Indeed I am probably not even looking to do traditional reference management, but more to keep track of what I have already read so that I can find it later when I reed it for writing up. I am writing a tool called Qiqqa (www.qiqqa.com), to which I add functionality all the time whenever I reach a stumbling block in my reference management needs.
    To point 3 above – it does OCR on your PDFs so you can do a full text search and text export on even your most ancient PDFs.
    To point 5 – synching with the online cloud is almost done so that I can work form the lab, from home and from my laptop.

  6. Nicolas Fanget says:

    Now that’s a talk I’d like to attend, shame I’m not available then :-(
    About your point 2: some word processors do have some limited capacity to insert citations/footnotes, but that is not what they were designed for. In fact I think it is better that this function is fulfilled by the reference manager, imagine if updates to your reference manager were dependent on Microsoft Word being updated! The current system with plug-ins is much more flexible.
    @Jimme I like the fact that qiqqa would  OCR my PDFs, I’ll have to give it a spin with my old papers…

  7. David Crotty says:

    What’s interesting to me is how many of the reference management systems see themselves more as “discovery tools” or “recommendation engines” than as organizational tools. I think that short sells the great value in an efficient organizational tool, and it’s a market that shouldn’t be overlooked. Researchers are increasingly dealing with large sets of information, whether it’s their reference list, the inventory of reagents in the lab, the lab’s current set of protocols or, probably the biggest and hardest of all to organize and store, data. If one of these companies can come up with an intuitive and easy-to-use system for organizing your references, it’s a foot in the door for more and more use of that company’s tools in other places in the lab.
    Also of note–so far, every single biologist I’ve asked about reference managers uses EndNote (including those who use other tools like Papers or Zotero as well). It’s interesting how rarely it seems to get mentioned in discussions of reference managers, given how pervasive it is.

  8. Martin Fenner says:

    William and Duncan, this is not really a post comparing the different reference managers out there. Rather what you can do with reference management, and maybe also about functionality that we need, but that is not really offered by any of the current tools. One example: integration of Journal Table of Contents RSS feeds with reference managers.
    Nicolas, Microsoft Word 2007/2008 has limited reference management features. The interface is nice, but the functionality very limited. It would be great if reference managers could integrate with this functionality, rather than rolling their own Word integration.
    David, “Citavi”:http://www.citavi.com/en/index.html is popular in the German-speaking world, and has some very interesting organizational features. An English-language version and a Mac version are in the works.
    If you read this post carefully, you find a “link to a review”:http://dx.doi.org/10.1021/ci00010a601 for Endnote Plus from 1992. Since v. 2.10 released on Sunday, Endnote Web (which has most of the required features including a Microsoft Word plugin) is available for free (i.e. for everybody with a ResearcherID count).

  9. David Crotty says:

    Not meant as a criticism of your coverage Martin, which is generally very comprehensive.
    But so often, the conversation around these new tools seems to fail to bring up the 800 pound gorilla in the market. It’d be kind of like reviewing search engines and not mentioning Google.
    Of course, the big difference with Google, is that I can’t think of anyone I’ve spoken with who actually likes EndNote. Given that animosity, it’s odd that none of the contenders has made much of a dent in their monopoly chokehold on researchers.

  10. Martin Fenner says:

    David, a blog post about Endnote is actually on my agenda. It will appear when Endnote X4 is released this summer.

  11. Nicolas Fanget says:

    Martin, you’d need someone even geekier than me to explain why sofware devs do not use the integrated bibliographic functions of Word and OpenOffice Writer. I guess the main reason is that they would have to tinker too much with it, and it could break whenever an update is made. I like it the way it is, it makes the software more portable.
    And good news, CSL 1.0 now supports superscript, subscript, small capitals, italics and boldface, so you should see this come to Zotero as well!

  12. Nicolas Fanget says:

    I forgot, the link to the CSL good news is here.

  13. Susan Steinhardt says:

    Martin, what great overview of reference management as well as interesting ideas for their future. What do you think of a laboratory or project management tool that incorporates reference management? Have you seen BioKM (www.biodata.com) which does exactly that (specifically with EndNote). Definitely makes it easier to see the big picture of your research!

  14. Martin Fenner says:

    Nicolas, I think it would be very helpful if word processors had a standard API for reference management. Not only would this cut down on development time, but it would also make it easier to use more than one reference manager – the Microsoft Word Plugins for Zotero, Mendeley, Endnote and Refworks don’t like to be installed on the same computer and sometimes interfere with each other.
    Susan, thanks for your comment. It would be helpful if you tell us in your comment that you work for BioKM.

  15. Nicolas Fanget says:

    Ah yes of course, but when are Apple (Pages), MS (Word) and Oracle (Writer) going to sit down and work out a standard API that works on all three very different software, all to satisfy what really is a minority of their users? In the meantime I think the plugin solution is really the least worst option. At least the bugs can be acted on by the ref manager devs, and they don’t need to rely on the big company’s approval.
    I understand that if you disable all your plugins and activate them only one at a time it should avoid most problems, but it looks like you have a very crowded computer 😉

  16. William Gunn says:

    Can’t wait to see your post on Endnote, Martin.
    To address David’s point above about services selling themselves as discovery tools rather than organizers, I have to say that Mendeley does very much sell itself as an academic paper organizer. We often use the phrase “itunes for research papers” to describe Mendeley, because that’s the most obvious and immediate benefit to someone who’s not familiar with crowdsourcing.