StructureDB - A Profiling Session

January 08, 2010

StructureDB - a profiling session

I came across this intriguing presentation, apparently by Jonathan Alvarsson, while doing some research on Mychem. Although the context is not described in detail, the fundamental problems should be familiar to anyone who has built a chemical database.

For those who may not know, Mychem is is an open source cheminformatics extension for MySQL based on Open Babel. From the about page:

... This extension provides a set of functions that permits to handle chemical data within the MySQL database. These functions permit you to search, analyze and convert chemical data. ...

Mychem is one of a few approaches to providing free chemistry database "cartridge" functionality that are now available. Others include OrChem and Pgchem. Each of these projects extends the underlying database to enable seamless integration of cheminformtics functions alongside those provided natively.

It turns out that this find coincided with a recent question posted to BlueObelisk Exchange asking about the best free tools for structure database search.

If you've built a chemical database, what technologies did you use for integrating chemical structure data with non-structure data and why?