Chemistry publication - making the revolution

Steven Bachrach has just published a very interesting commentary "Chemistry publication - making the revolution" on March 17, 2009 in the new Journal of Cheminformatics (I am on the editorial board).

The article does a great job of highlighting the current state of affairs in chemistry which is creating a chasm between researchers and the data they could be using. There are suggestions of steps that can be taken by researchers, reviewers and editors. Although Open Notebook Science is mentioned, there are several less intensive steps that can be taken to still benefit the community. Steven mentions the submission of JCAMP-DX files instead of PDFs when submitting spectra as supplementary materials for publications. I agree that this is a very low barrier step that chemists can take to gain immediate benefit - whether they share their spectra or not. At that point it also becomes trivial to contribute spectra to databases like ChemSpider that supports the open JCAMP-DX format - hopefully as Open Data (so that it can be used in applications such as our SpectralGame)

Spectral Game update

The end of February 09 has come and gone and nobody hit the 100 points to win the molecular model kit I announced earlier for the Spectral Game. The highest score in that time period was 75.

Since my CHEM242 class is having 2 tests and one exam in the next 3 weeks I thought I would make the next prize available to them exclusively. The student from that class who scores highest by 9:50 Wednesday March 4, 2009 will win a molecular model kit. That happens to be the end of class on that day. The scores have been reset.

The game has been improved considerably during the past few weeks. A few security flaws were fixed, including modifying what metadata can be viewed via JSpecView and preventing the refresh button from selecting a new set of molecules. The game play was also changed to get increasingly more difficult over time, including adding more molecules and a timeout after the first set of ten spectra. This work was a collaboration between Andrew Lang, Antony Williams, Robert Lancashire and myself.

We are very excited by what we have put together so far. There are currently 457 H NMR, 389 C NMR, 11 IR and 29 NIR spectra. This is only possible because of people who submitted their spectra to ChemSpider as Open Data - please keep uploading!

The game has been played 1,824 times, viewing the spectra a total of 8,652 times - with a lot of curation by users. (If you see something wrong with a spectrum you can write a note and that helps us clean up the database). We have had 612 unique visitors from 37 different countries - a total of 13,919 page views in just over two weeks!

We now have a wiki with key links relating to the game. I also added the NMR notes from my CHEM242 class and we'll keep collecting resources. This could become a helpful resource to learn about NMR and practice it by playing the game.