Managing the sea of data: Mendeley and PubChase

By Razib Khan | April 10, 2013 12:16 pm

Every few months someone asks me what I use to manage my papers. Stupidly, I don’t use anything. Or I haven’t. Over the past few weeks I’ve been playing around with PubChase and Mendeley. You probably know of the latter, and the fact that it’s been purchased Elsevier. Elsevier is what it is. Mendeley on the other hand is a firm that I have a positive view of, in part because of their culture of openness and support for the free flow of information, but also due to the fact that I’ve known their head of outreach for ten years. You trust people, not things. Mendeley‘s not a charity, and I don’t begrudge them their new resources now that they are under the corporate wing of Elsevier. Whether you’re pessimistic or optimistic about their future, I think caution is warranted.

PubChase is a new outfit you probably have not heard of. It’s product is a bit beta-ish feeling to me. I’ve been testing it on and off for a while now, because I have known one of the scientists who works for them for about five years. There are a few things missing, which I’ve been curious about. For example, where is the extension to simply add papers via Chrome? When I inquired about this the response I got was that you could import your Mendeley citations into PubChase. Not totally useful for me, but with the controversy over Mendeley‘s new corporate patron, this is probably a good opportunity for PubChase to position themselves as an alternative.

The ultimate issue here is getting relevant signal from noise. Individual human curation is still useful (ergo, Haldane’s Sieve). I don’t follow too many people on Twitter in part because I don’t want to get overwhelmed. And my focus is more professional than personal, so I have a lot of genomics and evolution people.

In the future I’m going to look for applications which not only manage the sea of data, but help you navigate it. There are way too many papers I download and only see three or four years later as I’m cleaning out folders.

Note: EndNote and CiteULike too. Don’t have time to try everything. Though people who use EndNote tell me that they use it partly because they know how to use it well.

  • S.J. Esposito

    I struggle back and forth with managing all the papers that I download. I was using Mendeley for a long while, until I bought a new MacBook Pro… there is no support for the retina display, which makes the PDF viewer present crappy text and even crappier graphics. In all fairness, Mendeley support has told me that they are working on it, but I couldn’t stand to wait for the time being.

    I’m back to storing PDFs on my HDD, which is a pain for obvious reasons. Friends of mine are very keen on printing a majority of their readings out and doing things ‘the old fashion way.’ I’ve contemplated this as I do tend to engage better with a reading when it’s in my hand and note taking would be easier. The sheer cost of paper and ink, however, is a deterrent.

    • Mr. Gunn

      Sorry it took so long, but I’m happy to report that the latest release of Mendeley has Retina display support.

      • S.J. Esposito

        This is very welcome news. Thank you!

  • Mr. Gunn

    Thanks for the kind words, Razib!


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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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