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The contents of this poster

CML is based on the ideas and success of HTML and the WWW and might be thought of as 'HTML with some chemistry added'. This is a useful starting point, and recently (1995/8/20) we got approval to use HTML2.0 as apart of CML. CML will, however, need its own renderers (browsers) and so we cannot yet show you this part of CML. (One approach may be to use standard browsers with helper applications).

There are, however, major differences from HTML in that CML is requires strict adherence to SGML. (HTML 'ignores' unknown tags and bad syntax; CML will object.) CML relies heavily on the use of carefully structured glossaries rather than adding semantics to the language itself. This allows great flexibility in that the chemical community can add new terms or even glossaries without having to revise the language or modify the software. Special interest groups can devise glossaries without having to seek 'permission' from the CML project.

CML has been designed to cater for a wider range of structured datatypes than HTML (which deals primarily with hypertext (text, image, movie, audio). CML allows definition of:

• Numeric and string data in scalar, array, matrix or tabular form. The glossaries may contain run-time code (e.g. in tcl, perl) for validation or transformation of such data items.
• Molecular information (with sufficient power to represent the common molecular formats chosen in chemical MIME). This includes stoichiometry, connexion tables, crystallography, symmetry, chirality, atom and bond types, etc. Moreover it can be easily extended through the glossary mechanism to cater for an indefinite number of ATOM and BOND attributes. provision is also made for multiple observations of the same molecule (e.g. conformational analysis, molecular dynamics, NMR ensembles.)
• Scientific units are give special attention with a separate glossary. This will allow the development of code for automatic conversion.
• Certain specified files (e.g. chemical MIME types) can be included in CML files. Thus a CML file for a protein could contain PDB and SWISS-PROT files with accompanying hypertext
• NOTE: at present CML does not explicitly provide for chemical reactions and protein sequences. However we are optimistic that rapid progress will be made with them after the release of CML V1.0. We also have not catered for generic molecular structures (substructures, Markush types, combichem, etc.) and will invite discussion :-).

CML is still evolving rapidly and we are offering it as a project in which the community can join. Ideas are welcome, but contributions such as tools, glossary creation, program interfaces, viewers, etc. are even more valuable and we'd like to hear such offers. We propose to form an electronic project to develop CML in a rapid fashion and offers of financial or material assistance would be very welcome. The project will be open and not aligned to any particular interest groups.

Some starting points

• Introduction and Background CML and its relation to other markup approaches.
• The main CML site (with latest information) and a simple guide . Also contains complete PostScript documentation.
• A publication (J. Chem. Soc. Chem. Commun.) in HTML and its rendering in CML. Note that this paper contains all the data required to repeat the calculations described . This is a good place to start if you want to see 'what CML looks like' and what its power is.
• A demonstration of CML in action. You can submit a MOPAC calculation whose input and output are managed through CML interfaces.
• Mailing list for chemical MIME . CML is an integral part of the chemical MIME project and the early discussion is archived here in HTML. The mailing list is chemime@ic.ac.uk.
• The virtual hyperglossary (VHG) project. The VHG project arose out of the virtual protein structure course and the idea has been used in ECTOC and the forthcoming Electronic Glycoscience conference.
• More about the CML project . Here is a form where you can register your interest in CML and offer contributions.
• Talk to PM-R in BioMOO . PM-R will be available to 'talk' to the poster during 1995/8/21. In the telnet window enter:

  
  	guest <name>
  
  	@join petermr
  
  and then type your messages starting with ", e.g.
  
  "hello, may I speak to PeterMR
  
  

• Workshop on CML in CCC Erlangen in June 1995.
• Prototype CML viewer for 3-D molecular structure written by Omer Casher.

Discussion and Implementation

In order to demonstrate a "proof-of-concept", we have implemented this dtd into a modified version of the MOPAC 93 program, which can now both read and write its output in formally structured CML. Presently this system can receive MOPAC internal and cartesian co-ordinates as well as the CML output from a previous calculation. Calculations in this demonstration program have to be limited to a small selection of MOPAC keywords and molecules with 6 or less heavy atoms and no more than 20 hydrogen atoms. Errors are currently handled by MOPAC itself in the form of the original output file rather than the CML file, on the assumption that the final archival version will not contain errors relating to e.g. geometry definition, geometry optimisation, etc.

MIME Considerations.

CML Working Example

Applications of CML

1. Because of the structured form of CML, the distinction between input and output formats for programs can be eliminated. Thus the output CML of MOPAC can equally well be used as the input if desired, with appropriate editing of keywords etc. In theory, MOPAC CML could be equally appropriate as say Gaussian Input.
2. We view as a high priority the development of a CML rendering program. At its simplest, such program could extract the atom types and coordinates and display on the screen a rotatable image of the molecule. More sophisticated versions could search for say eigenvector tags, and compute and display molecular orbitals. Any property suitable tagged in the CML definition could in principal be rendered by a suitable CML viewer. If built on top of code capable of rendering the full HTML 2.0 dtd, then such a viewer would provide an integrated text, image and chemical viewing system.

   Because the content of a CML document is precisely defined semantically, high quality indexing can now be performed on molecular properties, and not just simple keyword strings. For example, one can envisage an indexing program such as Lycos indexing against a specifically defined dtd such as CML, thus allowing much richer structuring of chemical content. The lack of any mechanism to index such chemical content on the World-Wide Web is currently one of its most severe restrictions.

   The development of better chemical indexing methods would in turn lead to the possibility of automated glossary constructions, where hyperlinks between related documents could be automatically inserted by suitable programs or scripts.

3. Because CML is a superset of HTML , there is a greater possibility that existing editors (i.e. aswedit for editing HTML 3.0) and browsers (e.g. Arena for viewing HTML 3.0) could be adapted for use in this area. The introduction of object based computer operating systems based on compound document architectures such as OpenDoc and Taligent would allow facile integration of new component parts into existing systems.

Conclusion