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.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.
I am forever returning to PubMed data, downloaded as XML, trying to extract information from it and becoming deeply confused in the process.
Take the seemingly-simple question “how many retracted articles are there in PubMed?”
Before we start: yes, we’ve been here before. There was the Biostars question “Calculating Time From Submission To Publication / Degree Of Burden In Submitting A Paper.” That gave rise to Pierre’s excellent blog post and code + data on Figshare.
So why are we here again? 1. It’s been a couple of years. 2. This is the R (+ Ruby) version. 3. It’s always worth highlighting how the poor state of publicly-available data prevents us from doing what we’d like to do. In this case the interesting question “which bioinformatics journal should I submit to for rapid publication?” becomes “here’s an incomplete analysis using questionable data regarding publication dates.”
Let’s get it out of the way then.
File this one under “has troubled me (and others) for some years now, let’s try to resolve it.”
Let’s use the excellent R/rentrez package to search PubMed for articles that were retracted in 2013.
library(rentrez) es <- entrez_search("pubmed", "\"Retracted Publication\"[PTYP] 2013[PDAT]", usehistory = "y") es$count #  117
117 articles. Now let’s fetch the records in XML format.
xml <- entrez_fetch("pubmed", WebEnv = es$WebEnv, query_key = es$QueryKey, rettype = "xml", retmax = es$count)
Next question: which XML element specifies the “Date of publication” (PDAT)?
Several of these sources cite data from my humble web application, PMRetract. So now seems like a good time to mention that:
- The application is still going strong and is updated regularly
- I’ve added a few enhancements to the UI; you can follow development at GitHub
- I’ve also added a long-overdue about page with some extra information, including the fact that I wrote it :)
Now I just need to fix up my Git repositories. Currently there’s one which pushes to GitHub and a second, with a copy of the Sinatra code for pushing to Heroku, which isn’t too smart.
In a previous post analysing retractions from PubMed, I wrote:
It strikes me that it would be relatively easy to build a web application (Rails, Heroku), which constantly monitors retraction data at PubMed and generates a variety of statistics and charts.
“Relatively easy” it was. Let me introduce you to PMRetract, my first publicly-available web application.
Read the rest…
As so often happens these days, a brief post at FriendFeed got me thinking about data analysis. Entitled “So how many retractions are there every year, anyway?”, the post links to this article at Retraction Watch. It discusses ways to estimate the number of retractions and in particular, a recent article in the Journal of Medical Ethics (subscription only, sorry) which addresses the issue.
As Christina pointed out in a comment at Retraction Watch, there are thousands of scientific journals of which PubMed indexes only a fraction. However, PubMed is relatively easy to analyse using a little Ruby and R. So, here we go…
Read the rest…