Voices of Open Babel – how an Open Source initiative is supporting chemical information translation

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 Chemical 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:

Calming the Proliferation of Chemical Representations with Open Babel

Dr. Geoffrey Hutchison, Cornell University

Modern chemistry delivers a vast volume of data in many forms and representations. One key challenge to cheminformatics is not only the archival and analysis of chemical databases, but the interconversion of multiple types of chemical data. From simply reading molecular modeling results to representing experimental crystallographic results, an increasing number of incompatible file formats and representations exist for chemical data. New, flexible standards such as Chemical Markup Language (CML) and IUPAC Chemical Identifier (IChI) have been developed but are slow to be adopted.

The Open Babel project is an open source development effort to provide an open, cross-platform chemical software library for interconversion of chemical file formats, molecular representations, and other chemical data. The open source process allows for collaborative software development, thorough testing and rapid bug-fixing. The project aims to facilitate open chemical software development and conversion of legacy chemical data, as well as to provide an open "toolkit" for computational chemists and cheminformatics.

In an extended interview with Geoff Hutchison we also discussed many related topics including the issues involved in managing such an open source project, GPL licence issues, use of Open Babel with commercial software, extension to analytical chemistry data, relationship with other Open Source initiatives, and standardising on fewer file formats and representations.

Incompatible file and data formats are one example of a barrier, in this case primarily technical but also with culture, human nature and commercial roots, to knowledge transfer between different people, places and times in the product life cycle.  We are initiating a new project on this important topic “Integrating knowledge in the life science product life cycle” on the KM in Pharma and Life Sciences Hub at http://innovationwell.net/.

You can listen to the full talk of Geoff Hutchison and interview with audio on the eCheminfo Hub at
http://echeminfo.com/

Barry Hardy
www.douglasconnect.com