Wednesday, October 06, 2010

Cheminfo Retrieval Classes 1 and 2 in 2010

My first Chemical Information Retrieval class for the Fall of 2010 took place on Sept 23, 2010. This is the second time that I've taught the class as sole instructor and it was certainly convenient to have last year's wiki to build upon. The assignments are the same so it was helpful to be able to give students access to what students did last year as examples.

The key message from my introductory lecture was that it can be really difficult to find usable chemical information and that there are no shortcuts like relying on a true trusted source - those don't exist. I showed a few examples of emerging models - Open Access, Open Notebook Science, Collaborative Competition (like pharma companies sharing some drug data openly) and other Open Science initiatives.

I also announced that we would be doing something new in the Science3.0 theme (the semantic web). One of the assignments involves collecting 5 values from the literature for each of 5 properties for a compound of the student's choice. In addition to adding these values on the wiki, we will collect them in a format that is friendly to machines: a ChemInfo Validation Google Spreadsheet. Andrew Lang has agreed to help with adapting our previous code for solubility to creating web services for this application. For example, we can have a service that reports the mean and standard deviation for a particular property and chemical. Another could produce statistics for a given data source or compare peer reviewed vs non peer reviewed sources, etc. Since it will be possible to to call these web services from within a Google Spreadsheet or Excel it should enable much more sophisticated analysis of the data related to the "validity" of chemical information as it exists today.

I didn't record the first lecture but I have the slides below:
During the second lecture on September 30, 2010 I spent most of the time showing students how to use Beilstein Crossfire, SciFinder and ChemSpider to find values for chemical properties. The recording for the second lecture is available below:

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