Analysis of retractions in PubMed

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…

Improvements to the reference management workflow

I use Google Reader to subscribe to the RSS feeds from journals that interest me (see my public page). I’m also a big fan of CiteULike as a reference management system.

For a long time I’ve thought: it would be great if GReader handled journal articles more efficiently. Rather than going from link in GReader -> article at journal -> CiteULike bookmark -> back to GReader, how about “post directly from GReader?”

With Google Reader’s new send-to feature, you can do just that. See this forum post for the details. Also, take a look at this how-to for a quick way to post to CiteULike by entering a PubMed PMID, DOI or ISBN identifier in the address bar.

It would be too easy to rant and rave about this

Zotero is a marvellous, active open-source project, providing a Firefox extension that captures and formats bibliographic information from web pages.

Thomson Reuters describe themselves as “the world’s leading source of intelligent information for businesses and professionals.” Whatever. They specialise in closed-source, proprietary solutions which to my simple mind is at odds with a role as an information source.

Via FriendFeed from Rafael Sidi’s blog, I learn that Thomson Reuters are suing George Mason University, developers of Zotero, for “violating its license agreement and destroying the EndNote customer base”.

Here’s my simple, black-and-white view of the world. The greatest achievement of the internet is the potential to set information free. There are free-thinking, forward-looking organisations like GMU who see this potential and act upon it. There are also organisations who see only threats to their corporate interests. Publishing corporations no longer control the flow of information to consumers and some of them seem to be struggling to accept this, adapt and move on.

As I say, too easy to rant and rave. If you’d like to do so in the comments, feel free.


It’s online, so I guess I can tell you about:

Lonic, A. Barry, E.F., Quach, C., Kobe, B., Saunders, N.F.W. and Guthridge, M.A. (2008)
FGFR2 phosphorylation on Serine 779 couples to 14-3-3 and regulates cell survival and proliferation.
Mol. Cell. Biol. (ahead of print); DOI:10.1128/MCB.01837-07 [Abstract] | [Manuscript]

A minor contribution from me: they asked which kinases might phosphorylate S779, I gave them a list (using a tool that may see the light of day eventually), they showed that activation of a candidate kinase leads to increased phosphorylation. That would rate an acknowledgement from some people, but these guys were kind enough to add our names to the paper.

Just another scene from the life of the “go-to” bioinformatician.


From Greg Jordan via the CiteULike discussion forums:

I thought I’d share with you a little tool I wrote to make working with CiteULike a little more user-friendly. It’s called SyncUThink, and it aims to do two things:

1. Search for, and upload to CiteULike, PDFs for all citations in your library.
2. Download all available PDFs to your computer.

I have it running now. The first attempt crashed my browser (not uncommon with Firefox + Linux + Java apps, unfortunately), but it seems to be running smoothly. I’ll keep you posted – this could be a really useful tool, provided of course that your network has full access to online articles.

Update: pretty good job. 100 PDFs retrieved for 153 citations and at a cursory glance, only one incorrect PDF was fetched. PDF download to an NFS-mount location failed, but seems OK to a local drive. However, if “tag subfolders” is selected, PDFs with multiple tags are downloaded to every folder with those tags which seems wasteful.

LaTeX tip: make your own styles

Last year I wrote a short post with some ideas on how to generate citation styles. The idea being that whilst there are many styles of referencing in different journals, there is a finite set of elements: plain, bold or italic; all authors or et al. after 3; volume + number or just volume and so on and so on. Computationally, it should be possible to construct a set of questions based on these elements and have a style pop out the other end.

Well, since then I’ve moved to LaTeX and of course, it does precisely this for you. Just “latex makebst”, answer a long series of questions and you’ve got a custom .bst file. More details are available at the LaTeX Bibliography Styles Database.

Getting started with Zotero citation styles

Any bibliography management system needs a good selection of citation styles and/or an easy way for users to add their own. As an incentive to write that Nature paper, Zotero now includes a Nature journals style.

I think it would be great if the bioinformatics community contributed some useful styles to Zotero. The process is not well documented, but goes something like this.

Read the rest…

Zotero now scrapes even more sites

Just noticed that Zotero now grabs articles from the BBC News website. Not especially useful for journal articles but nice to know, nevertheless. The latest Zotero-compatible sites are summarised in their blog.

A lot of their focus just now seems to be on developing as many scrapers as possible, which is not a bad thing but I hope it’s not at the expense of other feature development. I’m hanging on for network synchronisation and Connotea connectivity.

From the Zotero blog

I’m a big fan of the Zotero extension for Firefox. Old news from their blog earlier this year:

Currently there are several teams of developers working to integrate Zotero with popular social bookmarking sites like and reference management sites like Connotea.

This is tremendously exciting. You’d be able to search PubMed, one-click save using Zotero, sync your references to a shared, online resource and grab them back for citation in various formats. That’s pretty much the holy grail of reference management and bibliography as far as I’m concerned.