In the biblical story “The Tower of Babel” man’s ambition to create a world with one language and one speech was thwarted by divine intervention. Man was scattered across the earth to speak in multiple languages and men were no longer able to universally understand each other.
In our modern software environment it is man and woman, academia and industry, which has created a diverse multilingual environment and the challenges posed in integration and inter-system communication is a beast of our own creation and not the decree of some Incompatibility God! In the specific area of chemical information we do not yet have any universally agreed and widely accepted standards for the description of chemical information, be it on molecules themselves or on their calculated or experimental properties from analytical experiments in the laboratory. (There are initiatives in progress such as Peter Murray-Rust’s chemical markup language (CML) initiative but at least up to now implementation has often been lacking.)
A classic example of the chemical incompatibility disease is in the area of chemical structure file formats. We have a slew of many dozens of file formats each which take a different approach or emphasis to the description of molecular structures. The input to or output from one modelling program can hence be unintelligible to another, leaving us with the painful task of file conversions. The chemistry researcher is left mired as translator in this chemical hell of many voices, rather than spending productive time in executing programs and analysing data.
But there is a Chemical Saviour at hand in the form of an Open Source initiative and software called Open Babel. Open Babel translates many chemical structure file formats from one format to the other. Geoff Hutchison (Cornell University) is the project maintainer for this important and very useful program and presents the following seminar “Calming the proliferation of Chemical Representations with Open Babel” on eCheminfo (http://echeminfo.com/) starting 31 May which explains the project, program and approach: