Open Access News

Richard Noorden, Surfing Web2O, Chemistry World, December 2007.  Excerpt:

The rapid evolution of the world wide web is creating fresh opportunities - and challenges - for chemistry....

• The internet is becoming flooded with free chemical information: from blogs to videos and databases

• Linking this data together and interacting via the 'social web' could revolutionise the practice and teaching of chemistry 

• So-called 'Open Chemistry' faces many challenges: not least maintaining data quality and co-existing with trusted subscription databases...

[Jean-Claude] Bradley's idea is simple: most failed experiments are discarded, yet their data could be useful to someone else. Even published papers don't always sufficiently explain the workings behind a successful experiment. In contrast, all Bradley's research and raw data is now documented transparently and almost in real-time. Anyone can see it, comment on it, and use it; and the internet is the perfect vehicle for hosting it. 

Open Notebook Science is just one of many new routes for chemical information to appear on the internet. From searchable molecular databases to the user-editable Wikipedia; from video recordings of experimental protocols to the informal news, gossip and argument posted on chemistry blogs; a huge amount of chemistry can now be retrieved at no cost....

In this 'social web', swamps of data could be powerfully linked together. Search engines can trawl it to pick out whatever another user asks for. And user 'tagging', together with underlying machine-readable descriptions, means that related information can be easily linked. For example, clicking on a molecule could eventually bring up not just a 3D picture and a list of properties, but also the related online articles, experiments, videos and blog posts that refer to it....

'Mainstream chemistry has no tradition of openness and electronic collaboration. This is a bottom-up movement, largely composed of young researchers,' explains Peter Murray-Rust, a chemical informatics academic at the University of Cambridge, UK, and a keen advocate of what he terms 'Open Chemistry'. 

But as Murray-Rust also admits: 'chemistry is the best subject to do this with, but the hardest to sell it to'. The open chemistry model has to prove its worth alongside trusted, high-quality subscription databases and journals.... 

[R]esearchers are beginning to post videos of their own experiments on sites such as the Journal of Visualised Experiments and SciVee....

One of the most speculative projects includes blogger Mitch Andre Garcia's nascent Chemmunity- which asks chemists to take part in 'a global collaboration to solve interesting and novel chemistry questions. We will take a chemistry question from hypothesis to peer-reviewed chemical paper with all Chemmunity participants in the author list or acknowledgements.' ... 

One effective example of how the web can enhance content has been provided this year by the RSC's Project Prospect, whereby electronic journal articles are enriched with extra computer-readable metadata. It means readers can click on named compounds, scientific concepts and experimental data in an article to download structures, understand topics, or link through to electronic databases like Iupac's Gold Book....  

[T]he greatest source of established free information for research chemists on the internet are the 60+ small open-access journals some delayed open-access archived journals and, especially, the free online chemistry databases that aggregate together information on millions of molecules.

PubChem, 'the granddaddy of all free chemistry databases', as former medicinal chemist Rich Apodaca puts it, allows users to search almost 11 million compounds. It is maintained by the National Center for Biotechnology Information (NCBI), part of the United States National Institutes of Health....

Open chemistry advocates are frustrated by the way chemical data is fragmented between different closed databases. They reluctantly concede that gaining 'Open Access' to chemistry journals is a tough cause to fight . But 'Open Data' is quite a different proposition - publishers could well restrict access to journal papers while still freeing online records of their molecules and spectra, for example. 

The possible benefits of this approach to the chemical community are already apparent, via an online service called ChemSpider, which launched in March 2007....

Murray-Rust's own CrystalEye project is aggregating x-ray crystal structures, from the CIFs (crystallographic information files) that publishers demand as supplementary material for online articles. These don't fall under copyright laws, so it is possible to build up a free online database of crystal structures, even though they belong to closed-access papers.... 

[Y]et, Bachrach insists, the biggest problem is cultural - persuading chemists that they would benefit from access to other people's data is not easy, particularly as many chemists already have access to paid-for databases. 'Chemistry is a conservative subject,' fumes Murray-Rust. 'The chemical information market is now holding back opportunities.' ...