Subject: Re: CCL:(chemical) markup languages for writing scientific documents

From: "Dr P. Murray-Rust" <[email-masked]>
Date: 01 Apr 2003 12:01:15 +0100

On Mar 31 2003, Marc Baaden wrote:

> 
> Dear colleagues,
> 
> [email-masked] said:
> >> On more directly Web related matters,  two sessions at the ACS had
> >> relevance, one on  XML in Chemistry, and another on "The Scientific
> >> Article in the digital World".
> 
> > .. not immediately directly related, but still of relevance (I hope): 
> > what
> kind of authoring environment would be best adapted to the task of
> writing scientific papers, reports, abstracts etc. ?
> 
> I have recently been playing around with docbook and refdb (both come in
> SGML and XML flavours), and was amazed how far one could get with those
> already.
> 
> Especially for *computational* chemistry, docbook has all the nice tags
> for inclusion of code, screenshots, etc.

XML can revolutionise any scientific domain as it encourages 
interoperability through consistency of syntax and sharable ontologies. 
This is already happening in biosciences and we believe that it can do the 
same for comp chem.

At the ACS meeting Henry Rzepa and I and presented our extensions to CML 
(Chemical Markup Language) which may answer some of these questions. We are 
close to a distribution kit for which the current position is: 

- CML has been widely tested and implemented for managing molecules and 
their properties, both experimental and computed. Many of the OpenSource 
toolkits (e.g. OpenBabel, JChemPaint, Jmol, CDK, JOElib, bkchem, etc. ) 
support both input and output of CML. [We would be happy to hear from 
authors of such systems and advise them on implementing CML]. There is an 
open CMLDOM in JUMBO4. CML2 (CML is schema form) is available and a 
publication has been accepted for J. Chem. Inf. Comp. Sci.

- CML interoperates with most major XML languages, especially DocBook, 
XHTML, SVG (for graphics) and MathML for parsable maths. We have proof of 
concept for compound documents such as theses, journal articles and 
compound data cards.

- CML has been extended to reactions (CMLReact) and we are currently 
working with the EBI (Eur. Bioinf. Inst.) on enzyme-based reactions.

- CML can manage spectral data (CMLSpect) including annotation of peaks and 
peak groups

- CML has been extended to computational chemistry (CMLComp) to provide an 
infrastructure for the computational process. This includes job control and 
input, program output, XMLisation of manuals (so far MOPAC and GULP) and 
creation of ontologies (dictionaries) - generally one per program. We would 
be happy to hear from early adopters and program authors who wish to 
explore XML for comp chem. We are also developing Java, C and F77 libraries 
for XMLising program output.

CML home page is http://www.xml-cml.org and software/specifications will be 
distributed from http://cml.sourceforge.net.

Peter Murray-Rust