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The Chemical Markup Language

© Adam Hughes

In the last couple of articles, we've developed the basic principles behind XML, the Extensible Markup Language to lay the groundwork for examining CML, the Chemical Markup Language. This week, we'll look at some of the specifications of CML and then spend a couple of articles delving a little deeper to see what progress has been made and what practical applications have been affected by the advent of CML.

The concept of CML was first presented by Peter Murray-Rust, Henry S. Rzepa, and Christopher Leach at the 210th American Chemical Society Meeting in Chicago in August of 1995. In their poster presentation, they expounded on the motivation behind CML and also proposed some potential components of CML as well as applications that might make good use of CML. We'll review the highlights here, but the full document is available online at http://origin.ch.ic.ac.uk/cml/#intro.

As was mentioned in the first article in this series, there has been a lot of effort invested in the development of various data layouts for use in transferring chemical information among different parties. When CML was born, there had been recent undertakings to create sets of standard file descriptors for this purpose. Until that time, these efforts had focused on the extension of STAR and ASN.1 notations, but the CML developers recognized the emergence of SGML, the Standard General Markup Language, upon which was built the web-important HTML (Hypertext Markup Language). In fact, the HTML dtd, or "document type definition" was the basis for the CML definition.

The CML definition was developed to be component-based so that features could be easily added and subtracted without destroying the entire construct of the language. The initial list of desired features included a CML browser, CML rendering tools, a CML file generator, CML file-management tools, a CML file-authoring tool, chemical perception software, CML interfaces to popular software packages, and CML subject area glossaries.

It should be noted that CML was conceived from a theoretical chemistry point of view, which is fairly obvious from some of the items listed above. Indeed, the production of the above suite of tools into one package could very well be a sort of "dream team" for the computational chemist. The scientist would have at his disposal a friendly interface to a flexible data marking system that could interact, either as input or output, with the many different programs that he might wish to use in his research. What could be better?!

Obviously, because of the potential power of such a tool, the future applications considered were fairly ambitious. Some were alluded to above, but those outlined by the

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