Abstract word clouds using R

A recent question over at BioStar asked whether abstracts returned from a PubMed search could easily be visualised as “word clouds”, using Wordle.

This got me thinking about ways to solve the problem using R. Here’s my first attempt, which demonstrates some functions from the RCurl and XML packages.

update: corrected a couple of copy/paste errors in the code

Create your own Google Scholar RSS feed

Google Scholar is a useful tool and now has a dedicated blog. The first post is dedicated to email alerts.

It’s unimaginable, in 2010, that an alert service would not provide an RSS feed, so I can only assume that this feature will appear “in due course”. In the meantime, a quick Google search for create rss feed from website lead me to 7 Tools To Make An RSS Feed Of Any Website. I quickly tested them all and I agree with the author of the article: Feed43 is the winner.

The process for creating a Google Scholar feed is a little complex. Here’s my first attempt.

Update: interesting FriendFeed thread, where people point out that (a) scraping Google Scholar is quite likely to fail and (b) this is not the same as an alert, since results are not ordered by date.

ScienceRoll Search

Unhappy with PubMed or the other biomedical search engines?

Bertalan has created ScienceRoll Search, described in his blog post.

I just gave it a quick run and it looks rather impressive. Give it a go and let him know what you think.

GoPubMed

Sometimes it takes a while for information to sink in. Having read posts by Bertalan, Deepak and now Frank on the topic of GoPubMed, I finally got around to looking at the site.

If all interfaces to biomedical databases were as good as this, we’d all be happier and more productive. Go and try it out if you haven’t yet done so; it’s a really impressive piece of work.