better tools for mining the scientific literature

Freethinker’s Asylum has a great post reviewing a number of tools designed to help researchers mine the scientific literature–an increasingly daunting task. The impetus for the post is this article in the latest issue of Nature (note: restricted access), but the FA post discusses a lot of tools that the Nature article doesn’t, and focuses in particular on websites that are currently active and publicly accessible, rather than on proprietary tools currently under development in dark basement labs and warehouses. I hadn’t seen most of these before, but am looking forward to trying them out–e.g., pubget:

When you create an account, pubget signs in to your institution and allows you to search the subscribed resources. When you find a reference you want, just click the pdf icon and there it is. No clicking through to content provider websites. You can tag references as “keepers” to come back to them later, or search for the newest articles from a particular journal.

Sounds pretty handy…

Many of the other sites–as well as most of those discussed in the Nature article–focus on data and literature mining in specific fields, e.g., PubGene and PubAnatomy. These services, which allow you to use specific keywords or topics (e.g., specific genes) to constrain literature searches, aren’t very useful to me personally. But it’s worth pointing out that there are some emerging services that fill much the same niche in the world of cognitive neuroscience that I’m more familiar with. The one that currently looks most promising, in my opinion, is the Cognitive Atlas project led by Russ Poldrack, which is “a collaborative knowledge building project that aims to develop a knowledge base (or ontology) that characterizes the state of current thought in cognitive science. … The Cognitive Atlas aims to capture knowledge from users with expertise in psychology, cognitive science, and neuroscience.”

The Cognitive Atlas is officially still in beta, and you need to have a background in cognitive neuroscience in order to sign up to contribute. But there’s already some content you can navigate, and the site, despite being in the early stages of development, is already pretty impressive. In the interest of full disclosure, as well as shameless plugging, I should note that Russ will be giving a talk about the Cognitive Atlas project as part of a symposium I’m chairing at CNS in Montreal this year. So if you want to learn more about it, stop by! Meantime, check out the Freethinker’s Asylum post for links to all sorts of other interesting tools…

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