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

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 PostGenomic.com. 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*.acs.org/*
• http://www.rsc.org/*
• http://www*.interscience.wiley.com/*
• http://www.nature.com/*
• http://*.oxfordjournals.org/* (Added 01/May/07)
• http://*.plosjournals.org/*
• http://www.pnas.org/*

Here's the obligatory screenshot showing a recent issue of Nature containing quotes from both Chemical Blogspace and Postgenomic:

Correction/Retraction Notice

"This article has been corrected, partially retracted or retracted in full. See below for the link to the original article and the correction or retraction notice."

Update: I am continuing to add retraction notices to this blog post

If you are browsing the Table of Contents (TOC) of an ACS journal online, and you come across an article which has subsequently been corrected or retracted, why doesn't the ACS provide a link to the retraction? And similarly, why doesn't the retraction carry a link to the original paper?

Thanks to Chemical Blogspace and my Greasemonkey script, the blogosphere can collectively do what the ACS fails to do. What do I mean? Well, both Peter Murray-Rust and ChemBark have recently blogged about corrections/retractions by Sames and Sezen, so I looked up some of the relevant papers and listed them at the end of this blog post. In a few days time once this post has been absorbed into Chemical Blogspace, if you go to the ACS website to download one of these papers, you should see a CB icon which contains a popup referencing this post. By clicking on the link, you will be directed here and you can search the list below to find the link to the correction/retraction.



Corrections/Retractions:

Site-Specific Phenylation of Pyridine Catalyzed by Phosphido-Bridged Ruthenium Dimer Complexes: A Prototype for C-H Arylation of Electron-Deficient Heteroarenes
Godula, K.; Sezen, B.; Sames, D.
J. Am. Chem. Soc.; (Communication); 2005; 127(11); 3648-3649.
Correction/Retraction

Selective and Catalytic Arylation of N-Phenylpyrrolidine: sp3 C-H Bond Functionalization in the Absence of a Directing Group
Sezen, B.; Sames, D.
J. Am. Chem. Soc.; (Communication); 2005; 127(15); 5284-5285.
Correction/Retraction

Oxidative C-Arylation of Free (NH)-Heterocycles via Direct (sp3) C-H Bond Functionalization
Sezen, B.; Sames, D.
J. Am. Chem. Soc.; (Communication); 2004; 126(41); 13244-13246.
Correction/Retraction

Cobalt-Catalyzed Arylation of Azole Heteroarenes via Direct C-H Bond Functionalization
Sezen, B.; Sames, D.
Org. Lett.; (Letter); 2003; 5(20); 3607-3610.
Correction/Retraction

Diversity Synthesis via C-H Bond Functionalization: Concept-Guided Development of New C-Arylation Methods for Imidazoles
Sezen, B.; Sames, D.
J. Am. Chem. Soc.; (Article); 2003; 125(35); 10580-10585.
Correction/Retraction

Selective C-Arylation of Free (NH)-Heteroarenes via Catalytic C-H Bond Functionalization
Sezen, B.; Sames, D.
J. Am. Chem. Soc.; (Communication); 2003; 125(18); 5274-5275.
Correction/Retraction

C-C Bond Formation via C-H Bond Activation: Synthesis of the Core of Teleocidin B4
Dangel, B. D.; Godula, K.; Youn, S. W.; Sezen, B.; Sames, D.
J. Am. Chem. Soc.; (Communication); 2002; 124(40); 11856-11857.
Correction/Retraction

C-C Bond Formation via C-H Bond Activation: Catalytic Arylation and Alkenylation of Alkane Segments
Sezen, B.; Franz, R.; Sames, D.
J. Am. Chem. Soc.; (Communication); 2002; 124(45); 13372-13373.
Correction/Retraction

Added 01/06/07A Protein Folding Degree Measure and Its Dependence on Crystal Packing, Protein Size, Secondary Structure, and Domain Structural Class
Estrada, E.
J. Chem. Inf. Comput. Sci.; (Article); 2004; 44(4); 1238-1250.
Correction/Retraction

Chemical textbook blogging

By way of Peter Murray-Rust's blog (whom it's great to see back blogging), I came across a link to a Reactive Reports interview with Steve Bachrach who is the process of publishing a textbook entitled "Computational Organic Chemistry". One of the most interesting aspects of the discussion is that in order to keep readers of the book up to date, he has started a blog. Presumably, this will also form the basis of a subsequent edition of the textbook.

Blog entries on particular topics include full literature references with DOIs, as well as molecular citations using InChIs. If Egon adds this blog to Chemical Blogspace, it will be a valuable source of information for annotating molecules (via the InChI) and papers (via the DOI, and the Chemical Blogspace Greasemonkey script).

I wonder if the text of Open Access journal articles can be mined in the same way by Chemical Blogspace? This would allow users, while browsing the table of contents pages of any journal, to see whether any Open Access articles cite it, and to see the relevant quotes from that article.