A brief message for anyone who uses my PubMed retractions report. It’s no longer available at RPubs; instead, you will find it here at Github. Github pages hosting is great, once you figure out that
docs/ corresponds to your web root :)
Now I really must update the code and try to make it more interesting than a bunch of bar charts.
Just a quick update to the previous post. At the helpful suggestion of Steve Royle, I’ve added a new section to the report which attempts to normalise retractions by journal. So for example, J. Biol. Chem. has (as of now) 94 retracted articles and in total 170 842 publications indexed in PubMed. That becomes (100 000 / 170 842) * 94 = 55.022 retractions per 100 000 articles.
Top 20 journals, retracted articles per 100 000 publications
This leads to some startling changes to the journals “top 20” list. If you’re wondering what’s going on in the world of anaesthesiology, look no further
(thanks again to Steve for the reminder).
Back in 2010, I wrote a web application called PMRetract to monitor retraction notices in the PubMed database. It was written primarily as a way for me to explore some technologies: the Ruby web framework Sinatra, MongoDB (hosted at MongoHQ, now Compose) and Heroku, where the app was hosted.
I automated the update process using Rake and the whole thing ran pretty smoothly, in a “set and forget” kind of way for four years or so. However, the first era of PMRetract is over. Heroku have shut down git pushes to their “Bamboo Stack” – which runs applications using Ruby version 1.8.7 – and will shut down the stack on June 16 2015. Currently, I don’t have the time either to update my code for a newer Ruby version or to figure out the (frankly, near-unintelligible) instructions for migration to the newer Cedar stack.
So I figured now was a good time to learn some new skills, deal with a few issues and relaunch PMRetract as something easier to maintain and more portable. Here it is. As all the code is “out there” for viewing, I’ll just add few notes here regarding this latest incarnation.
Continue reading →