Home Science CommunicationScholarly communication How to get scientists to adopt web 2.0 technologies: reference managers

How to get scientists to adopt web 2.0 technologies: reference managers

by Eva Amsen

I spend quite a bit of time online. I have two blogs and a Twitter account, and through various services you can follow along with what music I’m listening to, some books I own, photos I took, or which sites I bookmarked.

I am aware that these things are public, and once in a while I might go through my Lastfm tracks to remove all evidence that I’ve been listening to something cheesy and embarrassing, or I’ll delete old tweets on Twitter. On my Flickr account, some photos are only visible to my friends and family who are also on Flickr. By default, all my Flickr photos are public, but I can manually set them to be only visible to friends. Sometimes I just want to upload a picture as a backup, and I’ll make it private so it doesn’t show up in my public feed at all.

Many, if not most, scientists are not in the habit of putting things online. The ones that are might be tempted by the concept of sharing the papers they read, letting everyone look at their lab notebook, joining a forum or writing a blog. If you’re reading this in your RSS feed or clicked through from FriendFeed, you’re probably one of those people. But think about your friends and colleagues who only turn on their computer for work and e-mail. They’re not going to tag their favourite papers or discuss the process of research with total strangers on the internet. It’s an extra thing to do that’s not already part of their lives, and no matter how appealing they might find the concept of open data or sharing information, they won’t join these sites or movements because it’s not something they are already doing.

So what are they already doing? They all have a database of papers that they use to cite while writing manuscripts. Something like EndNote suits their needs quite well: it keeps a record of all the papers they have and have read, and once it’s time to write that paper or grant proposal, they can cite the papers directly in their word processing software with one simple click. EndNote was the first reference manager they used, it roughly does what they need, and there is no need to abandon it. There is absolutely no good reason for them to export their library and upload it to something like Connotea or CiteULike. It’s just extra work, and it doesn’t benefit their research. The easiest way to keep track of papers is for them to keep using the tool they’re already used to.

Now go back a few paragraphs and read what I said about Flickr. When I need to quickly upload or save a picture, I will upload it as a private photo to my Flickr account. I could also have uploaded it to my own web domain, which is what I would have done if I didn’t have a Flickr account, but the Flickr uploader is simpler and quicker and it does exactly what I want at that moment, so that’s the tool I used. This just happens to be the same tool that allows people to share their photos with the entire world, tag them, and favourite photos that others took. I don’t need all that when I just upload a picture as a backup, but it’s there, and Flickr has become my default photo-uploader, even for non-shared items.

Someone recently told me that many people use Flickr only for that purpose: to just have a repository of their photos online, and not necessarily to share with everyone. And it’s true: if you browse around on Flickr, you’ll find a lot of accounts with few friends, and photos with little description. But because the default setting on Flickr is to upload photos publicly, and because tagging is so simple, people will do it anyway. It’s no extra work on top of what they wanted to do, which was just to put their photos somewhere, and Flickr is a very simple way to upload photos somewhere, simpler than whatever photo albums people used before. Tagging and sharing just came with the package, so they’ll use that.

Imagine if there was a bibliography reference manager that keeps a record of papers read, and allows users to cite papers with one click of the mouse, but does all this in a simpler way than EndNote, and perhaps has one extra feature that people really need but that EndNote doesn’t have. For example: if you’re co-writing a paper with someone else, the EndNote library needs to be on two computers. You can export it, but it’s kind of unwieldy. It would be easier to have a common shared library that both computers could use to cite in their word processing software. If such a program existed, and if it was easier to use than EndNote, and cheaper (free, even), and transferring all references from one to the other was fast and simple too, then people would adopt this new tool. Until then, what they are already using (whether it’s EndNote or another similar service) does the job and there is no reason to switch.

Now imagine if this utopian tool they all switched to because it was so simple and fast and useful just happened to come with the default setting to share your entire collection of papers and prompted to quickly tag everything once you added it. People would leave the public setting on, and they would tag.

You see this happening on Flickr. If you ask people directly if they wanted to share their kid’s birthday party photos with the whole world, they’d probably say no – but there they are, sharing their kid’s birthday party photos with the whole world. They don’t really care either way, they just don’t want to make any effort on top of putting the photos in an album for Aunt Mildred and Grandma to see.

This would work in the perfect utopian reference manager tool too.

Scientists probably don’t really care if you see what papers they are reading most of the time, but they just can’t be bothered to upload them all to Connotea to share them with you, because they can’t easily use Connotea to cite these references in their word processing software. If the tool they used anyway for citing references made their library public by default, they would use it. Like Flickr, there would still have to be a way to make something “friends only” or completely private, because there are papers that you might not want your competitors to catch you reading, but might still be useful to share with students or colleagues. But most of their libraries – well, you generally know what people are working on anyway, but that library they have with all the reviews and papers in their field is now only on their computer. If you want them to recommend something to read, you have to ask. In a default public reference citation manager, you could just see what they had, and if they tagged it or organized it you could also find out their favourites.

But wait, there’s more! Once such a system catches on, and many scientists have their reference manager publicly available, you can also see how many libraries a certain paper is in, and use that as a possible alternative or addition to a citation ranking. It wouldn’t work right now, I think, because the people who use sites like Connotea or CiteULike are the people who are used to sharing and tagging. I’d be willing to take a bet that the average Connotea/CiteULike user is (a) younger than the average EndNote-only user and/or (b) more likely to work in a computer-related branch of science or in publishing or information sciences. You need a tool that is adopted by the masses before you can use reader numbers fairly. Flickr has been adopted by the masses, because it does what people want and it does it in a simple and effective way. The fact that it’s a web 2.0 tool is secondary to many of its users, but it still got them to share and tag.

Of the existing reference managers, which is likely to be this Flickr for references? I had a look at this list that compares reference managers, and noticed that there is a division between tools that make citing papers easy (Endnote, RefWorks) and tools that make sharing easy (CiteULike, Connotea). Either Endnote/Refworks need to have their next version a default shareable tool, or Connotea/CiteULike need to come out with a super simple tool to cite papers while writing that is at least as good as whatever tool people are using now.

To be honest, neither seems likely. RefWorks is the opposite of open right now: In 2006, Canadian universities moved their RefWorks libraries to a separate server to hide them from the US government. The web-based version of EndNote does not have as many functions as the standalone tool, so people will still want to use the non-web (read: never sharable) version. CiteULike doesn’t have as many functions as people might want either (no option to hide a reference) and neither CiteULike nor Connotea seem capable of offering a stable tool to interact directly with word processing software, which is the only reason anyone would want to switch from EndNote, so both are stuck with the web 2.0-savvy users who don’t mind that they have all their references in multiple places: one for sharing and one for citing.

The one tool which might soon be able to do both public sharing and citing is Zotero. It’s a Firefox tool, but Firefox itself seems to be becoming the default browser for many, so that might not be a problem. Zotero currently allows you to bookmark a reference straight from the website (Pubmed or the journal itself, for example) and it has options for tagging and integrates with word processors.

It isn’t yet able to make libraries public, but the existing system makes it much easier for users libraries to be made sharable than the system used by Endnote. It’s different than Endnote, so there is a slight learning curve, but it’s free, and all they would need to do to be the Flickr of reference software is make users’ libraries public, and wait for users to share their libraries with new users for easy collaboration. Flickr users didn’t sign up because some blogger told them to, but because their friends invited them to look at their photos. That’s the trick. Scientists will sign up for a service if their collaborator on a paper asks them to sign up to share their library.

Writing papers in a fast an easy way is what scientists want, and if that happens to come with tagging and showing their collection of papers to the whole world, they’ll do that too. Once that happens, the concept of sharing will become more mainstream, and opening lab notebooks and data sharing can follow.


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Pedro Beltrao August 19, 2008 - 6:59 PM

Connotea and CiteULike already work to highlight articles that are more interesting. The simple fact that someone bothered to tag it into their libraries, even if just one person, already provides some information. The “Impact Factor” for papers tagged in Connotea under the tag Evolution for 2007 would be around 16 (2313 citations in 2007 to 170 articles from 2005-2006).
In a conversation with Michael Nielsen at the biobarcamp we talk a bit about web tools and he was also arguing in the direction that you are suggesting. These web tools must, first of all, solve some problem the users need without needing to resort to “network effects”. Those benefits should come as a bonus.

Anna Kushnir August 19, 2008 - 7:30 PM

I agree with you whole-heartedly, Pedro. Web tools need to appeal first to bench scientists, not web-savvy techies.
Eva – Can’t one import straight into Connotea from Pubmed? I though that was a feature. In fact, I was under the impression that it could pull a reference from practically any page – even if that reference is just a URL.

Martin Fenner August 19, 2008 - 7:58 PM

Eva, thanks for the detailed post. I almost completely agree with you (“Online reference managers: not quite there yet”:http://network.nature.com/blogs/user/mfenner/2008/06/23/online-reference-managers-not-quite-there-yet). But Zotero is not on my list because it stores references locally – this makes it difficult to share them with others. I haven’t looked closely enough at some of the newer social networking tools for scientists that allow you to bookmark papers, e.g. “Mendeley”:http://www.mendeley.com,

Eva Amsen August 19, 2008 - 8:24 PM

Anna, yes, it can do that, but it doesn’t have the cite-and-write functionality that people want, so even though importing new references is easy, it’s still not worth it for most people to switch. (Personally I haven’t been able to *export* my Refworks library, otherwise I’d have things in Connotea, but I can’t be bothered to re-add my 400 refs.)

Anna Kushnir August 19, 2008 - 8:27 PM

Yes, that’s very true. That is a severe limitation on Connotea’s usability in every day science writing. Can’t believe Refworks won’t let you export! That seems criminal. And bizarre, really.

Duncan Hull August 19, 2008 - 9:07 PM

Hi Eva, nice post
_They all have a database of papers that they use to cite while writing manuscripts_
I think there are an awful lot of scientists (some quite senior) out there who don’t even use EndNote. They type their references by hand…

Eva Amsen August 19, 2008 - 9:14 PM

Re: refworks export – I can export a few at a time, but it’s very slow, and it crashes when I try to do everything at once. I can probably export everything as 20 groups of 20 papers, but can’t be bothered to do that.
Duncan, really? I’ve never met anyone without an EndNote library, I’ve met some old-fashioned scientists.

Frank Norman August 20, 2008 - 11:28 AM

I also agree with much of what you say Eva. It has been interesting to see how quickly Endnote are developing EndnoteWeb now in response to the competition from Refworks. We’ve talked with both companies and pointed out to them the pressure from tools like Connotea and I think they appreciate the need to match them.
For Open Office users it’s also worth keeping an eye on “OOoBib”:http://bibliographic.openoffice.org/ – the Open Office Bibliographic project. They promise something late 2008/early 2009.

Frank Norman August 20, 2008 - 1:05 PM

Note on Zotero. My colleague (Patti Biggs) tells me that the latest version seems much improved on recognising bibliographic references, but still has some problems with Web of Knowledge (in the “all databases” search) and with Zetoc. This contrasts with Endnote and its hundreds of connection files/import files.
There also seem to be some problems when you have the Zotero add-in to Word alongside Endnote.

Marc Sal August 20, 2008 - 2:31 PM

This is what we are trying to do at , providing a Scholar Directory, Open Access Repositories, and research sharing forums for all disciplines. At the very least, it would be a good idea to create a global scholar directory where you can type in a few keywords and bring up everyone who is doing research in an area you are interested in.

Björn Brembs August 20, 2008 - 2:02 PM

I’ve also met people who type their references from hand. few and far between, I admit, but they still exist. As you say, most people use their computers for storing and evaluating their data, literature searches (mostly blatantly ignorant of the many tools there are), writing papers and email. The huge majority have never heard of nn, facebook, friendfeed, twitter, etc.

Cameron Neylon August 20, 2008 - 2:44 PM

Interestingly enough I’m moving away from Endnote because I keep seeming to break it. But I haven’t yet found a solution that works. But I agree if citeulike and connotea could provide one click adding to library (which they do) and easy insertion into documents (which they don’t) then I think there would be a stampede. And then people would realise the social benefits. I think this was Michael’s point which you have articulated well. Whatever it is it has to work for me first, and then people will start to see the social side, not the other way round.
Just to add links because no-one else seems to have yet: Ian asked the question “we are having a serious think about Connotea. What would it need to do to be a killer app for helping scientists?”:http://friendfeed.com/e/843063fc-1a40-e206-e18b-3178f1577d18/we-are-having-a-serious-think-about-Connotea-What/ on Friendfeed and “on his blog here at NN”:http://network.nature.com/blogs/user/ianmulvany/2008/08/19/more-feedback-wanted-where-do-we-go-now and I made “my pitch here”:http://blog.openwetware.org/scienceintheopen/2008/08/19/how-to-make-connotea-a-killer-app-for-scientists/

Heather Etchevers August 20, 2008 - 8:59 PM

Yes! We DO need a citation tool that “does what people want and … in a simple and effective way.”
I’m also quite excited about Mendeley. Except that it automatically tags all those PDFs that you’ve already downloaded. I haven’t seen if it allows you to make an Endnote-like database (a program to which I have been faithful since version 2.0) but that would be just great if so. So in a perfect world, Connotea/CiteULike would do that too, retroactively as well as proactively – I have some 1700 PDFs lying around on my hard drive including new manuscripts and supplementary data from various articles that have been of interest to me, and of course that will be growing. I can’t tag the new ones and ever hope to catch up on the old ones manually.
Anyhow, Eva, great post.

Mounir Errami August 24, 2008 - 2:16 AM

very interersting posting. Take a look at CiteSmart (citesmart.com). Theoretically it can be interfaced with Connotea but it has been so far with Pubmed (and Ovid medline)… It works with IE, but a FireFox version is in the box (more later…).

Bora Zivkovic August 24, 2008 - 6:17 PM

There is also ‘Papers’:

But if iTunes gets serious about this, they would take over the market fast as even among scientists, more people are familiarized with the use of iTunes than any other potential paper-organizing software:

Eva Amsen August 24, 2008 - 6:41 PM

I tried Papers, but I don’t have that many pdfs on my computer and found it more useful to just save the links to where to find pdfs and get them when I need to. I always print them anyway, and have a pretty good paper filing system. (“Pretty good” right now means that there are piles of papers all over my living room floor, but the majority of piles are sorted by topic and I can actually find 95% of the papers I need.)

Graham Steel August 24, 2008 - 6:50 PM

Carbon of Bora above but with active links.
There is also “Papers”:http://mekentosj.com/papers/
But if iTunes gets serious about this, they would take over the market fast as even among scientists, more people are familiarized with the use of iTunes than any other potential paper-organizing software.
“For example”:http://scienceblogs.com/transcript/2007/04/organize_your_pdfs_with_itunes_1.php

Mounir Errami August 24, 2008 - 7:19 PM

I would tend to agree with Eva. Most of the pdfs are accessible online and it would more interesting if from a reference, a direct linked was saved automatically to access the paper (i.e for PubMed central this is easy, PubMed also provides a LinkOut feature that takes you to the website from which the paper can be accessed, depending on your organization subscription).
Besides dealing with papers locally and libraries may create some issues: how to organized them (keywords, tags, groups, folders?).
As long as users talk about using Connotea and others (2collab, Mendeley, bibSonomy etc…), then they will be online most of the time. Therefore, having papers locally seems just a waste of space, and time (download/organize/configure).

Heather Etchevers August 24, 2008 - 9:13 PM

Having papers locally means that you won’t have problems in our highly mobile profession when you move to an institution that doesn’t subscribe to the set your previous institution used to have. Of course, in a perfect world, the preprints are publicly available or all the articles you’d like are Open Access.
And it’s useful to be able to organize the PDFs you have requested from authors because no institutions with which you are affiliated subscribe to that journal at all. I don’t think it will be possible to access everything online, but storage on local hard drives is still better than printing it all out – I did that for a while, but wait until you move labs, Eva!

Bora Zivkovic August 24, 2008 - 10:30 PM

Links won’t do for me, except for OA articles. If I got a pdf from an author or friend, I need to have it myself. Sharing those, though, would probably violate copyright.

Mounir Errami August 25, 2008 - 12:00 AM

Agreed with you here. In certain circumstances, like author’s reprint etc, it is surely useful to have the paper stored. But, in my own experience, I hardly read the same paper twice. Alright there is the moving lab issue and institution subscriptions. Most institutions offer a wide coverage of the scientific literature (I am talking about Medline). So really, I personally don’t think that having each and all PDFs locally would help that much. In the past 5 years, most of the papers (over 90%) I read were online and accessible one way or another. Of course there is always this one paper that you can’t have, but does it justify try to get all of them locally, even when they are online and accessible? I don’t think it is worth my time to fight and organize a bunch of PDFs when they are 1 click away for the most part… But I agree that sometimes, the click won’t work (most of the times it will work though).

Graham Steel August 25, 2008 - 11:22 AM

Interesting discussion.
Zotero 2.0 sounds awesome.
_Of course, in a perfect world, the preprints are publicly available or all the articles you’d like are Open Access._
If “current trends”:http://publicaccess.nih.gov/ continue, ultimately, I sense that that’s very much where we’re heading to.
For example, have you seen “Repository 66”:http://maps.repository66.org/ recently?

Thanks for the i-Tunes suggestion Bora. Copied my entire PDF Library over to i-Tunes very easily last night and backed up a copy to CD.

Mounir Errami August 25, 2008 - 2:58 PM

indeed, there has been some interesting works published about “the advantage of Open Access”:http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0040157&ct=1 (and ultimately citation advantage, important for Impact Factor calculations). Besides, authors are more prone to pay for their papers to be published in open access (OA) than readers to pay to access it. I mean that if a journal has a mandatory open access policy (like PLoS for example), and a paper is accepted, the authors will surely pay the OA fee. Now I don’t know if from a Business plan perspective that works well for the journals.

Martin Fenner August 26, 2008 - 5:40 AM

I’m also a big fan of “Papers”:http://mekentosj.com/papers/. Storing PDFs locally is still important for a variety of reasons that have been mentioned already. It has two important shortcomings: 1) you need another program such as Endnote to integrate the references into the manuscript you are writing and 2) it has no online version which would allow sharing of references with others (the main point of this blog post). I will try to ask Alexander Griekspoor (one of the authors) at the Science Blogging London meeting about the plans for version 2.0.

Mounir Errami August 26, 2008 - 10:55 PM

I thought that Mendeley could help do that. I don’t use it. I am a fan of CiteSmart (obviously…), as it makes finding and citing refs easy directly from PubMed. As for PDFs, it is like with EndNote, you drag and drop them on a ref and it becomes linked to it. But no online sharing…

Victor Henning September 5, 2008 - 1:30 PM

I can’t believe I missed this blog post! Eva, you’re describing _exactly_ what we are trying to do with Mendeley. It’s uncanny! There’s an “interview on Martin Fenner’s blog”:http://network.nature.com/blogs/user/mfenner/2008/09/05/interview-with-victor-henning-from-mendeley where I go into a bit more detail on this – and that’s where I learned about this blog post, too…
Very much looking forward to meeting you in Waterloo next week!

Maxine Clarke September 14, 2008 - 6:46 PM

We just heard anecdotally from a couple of authors of consortia papers that there are issues with the PubMed export to EndNote not showing the citation correctly – might be worth checking out for those concerned about such matters.


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