Thursday 17 May 2007

Stack It! - Popularity voting for papers

Prompted by a blog post by Ψ*Ψ which referred to a reddit-style voting system for papers, and based on the excellent "Stack It!" feature of Ohloh, I've implemented a Stack It for journal papers using Greasemonkey:

All you need is an account at Connotea. The first time it runs on a journal web page, it asks for your Connotea username and password - this will be remembered until you close the browser. To stack your favourite papers, just click "Stack It!". To unstack, you'll have to log into Connotea. The tag "stackit" is used for all stacked papers.

It should be possible to identify other people with similar stacks to yourself, and see what else they have stacked (Ohloh can do this). Also, you could have an RSS feed to what people are stacking recently, or you could have a list of the most popular JACS articles in the last month.

Wednesday 16 May 2007

Framework for a commenting service

Over at Carbon-Based Curiosities there have been some interesting discussions on a social commenting service for journal papers. In addition, PMR has been discussing the merits and best methods to do standoff annotation of PubChem.

Here's a mashup method that would be suitable for both, and reuses existing technology so that only the glue needs to be written:
(1) Create a blog called
(2) Write a greasemonkey script (or Firefox extension) that adds a link "Comment on this" beside the title or DOI of the paper of interest
(3) When you click on the link, it creates a new blog entry for that paper or else brings you to the existing blog entry.
(4) You add your comments like in a normal blog, and click Save.
(5) The script in Step 2 should also flag any papers that already have comments

(1) Commenting is already well developed for blogs. There is anti-spam system in place. You can subscribe to comments on your own papers, etc.
(2) Moderation of comments is possible, although the entire chemical blogosphere would have to help out on this - no moderating of comments on your own papers, of course. :-)
(3) The Greasemonkey script for displaying comments from existing blogs does many of the same steps, and has shown that it *is* possible (not just pie in the sky). The chemical blogosphere is fewer than 100 people at the moment, whereas the potential commenters on papers is much larger.

(1) Users need Firefox, Greasemonkey and the Greasemonkey script.
(2) I think that it may require a standoff site (similar to Chemical Blogspace) to gather the list of existing comments and make it accessible to the Greasemonkey script via an API. However, I could be wrong. In any case, that is no big deal.
(3) The blog username and password would be contained in the Greasemonkey script for all to see. Can varying levels of permissions be set for different users of a blog? Alternatively, the blog entries could be created automatically based on RSS feeds from the journals, and so only the comments would be possible using the Greasemonkey script.
(4) Would probably need to develop a standoff backup service for comments, in the event of people deleting them. Not a big deal - possibly has already been done.

The main thing I'm worried about though is that this has already been done by Connotea. I'm not very familiar with Connotea - is that a better route for social commenting? I know that there are already some Greasemonkey scripts for Connotea - can you comment on a paper from a journal web page, and see existing comments?

Tuesday 8 May 2007

Supporting information available as text

"Supporting information is available for this article as text files. See below for the links."

Providing datasets as text files is much more useful than making them available as PDFfiles (hamburger, anyone?). Recently a colleague of mine, Dave Palmer, published a QSAR model of the aqueous solubility of organic compounds. I'm not sure whether at the time it was possible to provide the supporting information as a text file. In any case, the test and training sets are available on the ACS website as two PDF files rather than as text.

Thanks to the magic of the Chemical Blogspace Greasemonkey Script I can alert anyone who visits the journal website that the supporting information is now available as text files.

Supporting Information:
Training Set
Test Set

Tuesday 1 May 2007

Add quotes from PostGenomic and Chemical Blogspace to journal

Update 18 July 07: Updated address of Blue Obelisk wiki

Greasemonkey is a Firefox extension that allows you to rewrite the HTML of a webpage on-the-fly. Pedro Beltrão was the first to think of adding a link to journal Table of Contents pages whenever a particular paper had been reviewed on I extended Pedro's script to include a clickable pop up of the actual blog post as described by Egon.

I have just released a new version, described on the Blue Obelisk wiki and available from User scripts. This incorporates comments from both Postgenomic and Chemical Blogspace, although you can use the menu to choose just one or the other.

Feedback is welcome. In particular, what journals would people like to see added? Currently, only the following websites are included, although others may work if you add them (please let me know if they do):
  • http://pubs**
  • http://www**
  • http://** (Added 01/May/07)
  • http://**
Here's the obligatory screenshot showing a recent issue of Nature containing quotes from both Chemical Blogspace and Postgenomic: