Another diversion from the main theme of this blog.
I have been an advocate for a revolution in chemistry publication making use of the technologies available on the net. My latest polemic on this topic is “Chemistry publication – making the revolution” (DOI: 10.1186/1758-2946-1-2) where I advocate for inclusion of more data within articles, enhancing the reader experience by being able to manipulate the data in the same way that the author did. I argue for development of tools that will enable publication of data, along with chemical semantics. Peter Murray-Rust has blogged on perhaps the first step in this direction: Chem4Word.
I ran across a very interesting article on a similar topic in Learned Publishing. The article is “Semantic Publishing: the coming revolution in scientific journal publishing” by David Shotten (DOI: 10.1087/2009202, also available from this repository). Shotten is in the zoology department and so comes to the semantic web with a different perspective, yet arrives at a similar place that I and Peter Murray-Rust and Henry Rzepa (and other chemists) have been advocating. Shotten advocates for “live data” and semantic markup – and cites Project Prospect (the RSC markup of chemical documents built on PMR’s work) as an example of this. Shotten includes a link to a sample zoology article that his group has “enhanced” and there are a lot of clever additions that chemistry publishers would be well served to examine – links to data, cloud tagging, customizable references, etc. Check out the enhanced document here.
Perhaps a growing push for “enhanced publication” from many disciplines will spur on action among the major publishers!
Henry Rzepa responded on 07 May 2009 at 2:07 am #
The Semantic Web message has been preached for some little while now. I know this is blowing my own trumpet, but along with the excellent Shotton articles, you might be interested in a much earlier example of this genre published as long ago as 2001 which not only includes diverse kinds of chemical data, but generates an article from this data on the fly using XML/XSLT and Java technologies.
You might also be interested in our recent experiences with Elsevier as a publisher. We had submitted our usual data enhanced Web table accompanying the article, and although we were originally assured that handling it would be no problem, when the article was accepted and galley produced, we found to our dismay that all the data enhancements had been bundled off as a ZIP file in the supporting information. The explanation as I understood it, was that the article production system at Elsevier in fact adopts the same “just-in-time” processes as we had espoused in 2001. The only snag was that their XML markup did not include any appropriate data markup objects or namespaces (such as CML for example), and so no chemistry data could be entrained into any article via the XSLT produdtion processes. The only remaining formats were in effect Acrobat, and various movie formats (which in themselves are actually largely data free), none of which were in the least appropriate for us. So in the end, after much discussion to and fro, the data for the article now resides on the Imperial College server, very much NOT part of the main published article.
Postscript: In the article above published in 2001, many browser technologies for handling XML and XSLT on the fly were very immature. The system worked in IE 6.5, but sadly broke some time after. So whilst the data is still there, the technology for presenting it to the user is currently broken. We now refer to this article as the first example of necessary Internet archeology, where some repair work/preservation is now required to restore functionality. Would anyone like to volunteer?