Novelty: an update

A recent tweet:

@neilfws I enjoyed this: https://t.co/ynyHRbgpLN Have you published (or are you thinking about publishing) this analysis anywhere?

— Marcus Munafo (@MarcusMunafo) October 7, 2015

PubMed articles containing “novel” in title or abstract 1845 – 2014

made me think (1) has it really been 5 years, (2) gee, my ggplot skills were dreadful back then and (3) did I really not know how to correct for the increase in total publications?

So here is the update, at Github and the report.

“Novel” findings, as judged by the usage of that word in titles and abstracts really have undergone a startling increase since about 1975. Indeed, almost 7.2% of findings were “novel” in 2014, compared with 3.2% for the period 1845 – 2014. That said, if we plot using a log scale as suggested by Tal on the original post, the rate of usage appears to be slowing down. See image, right (click for larger version).

As before, none of this is novel.

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.