Subject: Release of CML2.0 (Chemical Markup Language) and Schema

From: Peter Murray-Rust <[email-masked]>
Date: Tue, 19 Nov 2002 09:59:10 +0000

The CML (Chemical Markup Language) DTD which has been in use for 3 years 
has now been upgraded to conform to the W3C [1] specification for Schemas. 
All specifications and software are OpenSource/OpenData.

The basic chemical concepts of CML are not significantly changed and 
Version 1 will continue to be usable. There are several advantages to Schemas:
- the syntax of CML documents is considerably simpler and less verbose 
(e.g. the "builtin" attribute is no longer necessary)
- there is much stronger datatyping; elements can be validated against the 
Periodic tables and floats, integers etc are fully supported
- they support XML namespaces so designs can be modular
- modern XML software concentrates on Schemas rather than DTDs

This has allowed us to create a modular design with the following components:
- CMLCore which is reused by other modules
- STMML [2] which supports numeric data, scalars, arrays, matrices, 
dictionaries, metadata and experimental procedures.
(CML also interoperates with major W3C languages such as XHTML, MathML and 
SVG [3]. With these complete chemical documents (such as publications) can 
be created, queried, processed and rendered.

Several other modules are under active development
- Computational Chemistry Markup Language (CCML) whose first phase is being 
presented to a CLRC [4] meeting of early adopters from UK eScience projects 
this week. CCML will be run as an Open community activity to develop XML 
support for all aspects of Computational chemistry. We shall announce 
details of the mailing list very shortly.
- CMLReaction. CML already supports reactions and this functionality is 
being refactored and expanded into a separate module.
- CMLQuery. This is being built on the emerging XML Query language

CML modularity relies heavily on the creation of dictionaries and we are 
part of the IUPAC XML Dictionary project.

The CML and STMML Schemas can be found as XML, XHTML and PDF[*] at 
http://www.xml-cml.org and will also be posted in the repository at 
http://cml.sourceforge.net shortly.  The distribution contains many 
examples of CML and STMML which have been validated against the Schema with 
3 independent toolkits [5]. Several OpenSource projects have early 
implementations of CML2 including OpenBabel, BKChem, and JUMBO.

Peter Murray-Rust
Henry Rzepa

[1] World Wide Web Consortium
[2] Scientific Technical Medical Markup Language
[3] Scalable Vector Graphics
[4] Central Laboratory of the Research Councils (UK)
[*] all specifications are autogenerated by XML technology.from the 
original schema document.
[5] Apache/Xerces, MSIE MSXML4, IBM Schema validator.