Chemical markup language

peter Murray-rust (
Wed, 3 May 1995 08:11:49 +0100 (BST)

I have hacked the next phase of the Markup. It is under:

I have taken a *data*file from Henry/Chris_Leach and marked it up in a
reasonable but arbitrary manner. Have a look and let me have your comments.
It allows for terms to be linked to a glossary, so if there were a
theoretical chemistry glossary it would be automatic to have links to
definitions of ionisation potential, etc. Also various types of data
item could be marked up (e.g. atomic coordinates could be rasmolified).

Herny, if you could think of perhaps 50 terms that a theochem glossary
requires and perhaps a markup of another file type (e.g. Gaussian) we
would then have a strong basis for a program-independent meta-language.
Note that the *programs* are exactly the same as used for created the
hyperglossaries - I haven't had to change a single line so we really have
got to discipline-independence. We also need a postprocessor for each
file type. In tcl that will take me about 1/2 day so long as the file
format is clear and not too context-dependent. (Note that the SGML
format allows for distributing the original file as well so that FORTRAN
junkies can read formatted linprinted output).

Lesley I'm conscious that I need the last 10% effort to get the
new SGML version working under HTML for entry creation. It's all there -
just needs a half day at BBK (it's so difficult to do the HTML
implementation remotely). I also haven't quite mapped out the name space
yet for cross references.


Peter Murray-Rust, Glaxo Research & Dev. (; (BioMOO: PeterMR)
Birkbeck College,, CBMT/Daresbury,