I think that for at least as many people that worry about it an equal number choose to use Connotea as they feel that by being backed by a publisher that has been around for some time there is an implicit guarantee that the service will be around for a while. In the year that I have been involved this is the 3rd time that I have explicitly addressed this question, and it is a fair one. Part of our answer to that is that our code is open source, and we have an open API into our data. One advantage to a product like this coming out of a publishing company is that we are interested in technologies around the full spectrum of scientific communication. Working with people who develop Nature Network, or who look at content matching will feedback into Connotea and make it a stronger product, at least I hope ;).While the open API gives Connotea an advantage over CiteULike (Citeulike: A Researcher's Social Bookmarking Service. Ariadne Issue 51 April 2007), in my view and in the view of some of those who contacted me privately, this is cancelled out by the fact that it is perceived as a tentacle of the "Nature Network" (network by name, but not by nature).
I've had chance to play a little bit with CiteULike now, and my feeling is that it's very similar to Connotea overall. In my limited testing, CiteUlike feels better than Connotea on spam links, and I much prefer the CiteUlike interface, without the spurious Nature crap and adverts which turn scientists off in a big way. The pdf upload option is also very attractive to many scientists. On balance, CiteUlike wins.
But here's the problem:
Almost all the people who emailed me privately said the same thing: I tried Connotea/CiteUlike a while ago, but I don't use them. I couldn't see the point. And there's a reason for that. If these sites are just filing systems into which people chuck references, they can't compete against existing systems in use such as EndNote, RefWorks, etc. The people who emailed me were not big social network users, and had not understood the resource discovery implications of a refined network such as one can build on del.icio.us (or Twitter).
Or had they?
Are either of these sites fit for purpose? Neither site feels like it has a big enough user base in the Life Sciences to make it of much use for resource discovery. And that's confirmed by this paper:
Content Reuse and Interest Sharing in Tagging Communities
Tagging communities represent a subclass of a broader class of user-generated content-sharing online communities. In such communities users introduce and tag content for later use. Although recent studies advocate and attempt to harness social knowledge in this context by exploiting collaboration among users, little research has been done to quantify the current level of user collaboration in these communities. This paper introduces two metrics to quantify the level of collaboration: content reuse and shared interest. Using these two metrics, this paper shows that the current level of collaboration in CiteULike and Connotea is consistently low, which significantly limits the potential of harnessing the social knowledge in communities. This study also discusses implications of these findings in the context of recommendation and reputation systems.
These numbers are trivial compared to del.icio.us (well over 2 million). But it gets worse. Scientists don't share. The above study finds: 1) consistently low levels of item reuse, (2) high levels of tag reuse, and (3) most activity being generated by existing users with little recruitment to a low base.
So here's the solution. Neither Connotea not CiteULike are fit for purpose, Even if they were to merge (which they won't), they probably couldn't overcome the damage they have done to social bookmarking in the Life Sciences. But there's one site which could. If PubMed were to add social resource discovery features, it would kick both Connotea and CiteUlike into touch, and possibly overcome the reluctance of self-absorbed bench scientists to share resources.
And until that happens, I'm not prepared to recommend either Connotea or CiteULike to undergraduates. I may recommend CiteULike to postgraduate and postdoctoral scientists as an alternative to del.icio.us - but only until PubMed introduces social resource discovery and sharing features, then it's game over.