Subject: bystander's look: XML as program output?

From: Christoph Maerker <[email-masked]>
Date: Wed, 19 May 1999 13:26:46 +0200 (MEST)

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Dear all,

may be the force with you and let you not implant surrounding sound in a 
well-known QM workhorse. (Sorry guys, I could not resist to write this TODAY).

Stepping in at such a late point about text vs xml, I would like to re-focus
attention to the point of "annotation", a widely-used term in bioinformatics
nowadays.

In this sense I agree with WDI that "tags are primarily for content 
decsription and not for formatting purposes". Given the millions of number-
crunching machines, sequencers etc, there is an ever-increasing flood of
digital information. Exa/Terabyte disk-farms could store all that, but the 
real problem is to find the gold-nuggets out of a heap of trash (I had no 
particular program in mind, I am honest). And for that purpose one needs
annotated data, maybe in the form of xml or any other commonly-used format
(NB I did not write agreed-upon standard).

Therefore, whether current QM codes get xml-enabled in one or the other way 
is not the main point. They will sooner or later, e.g. by simultaneously 
printing tags, either for direct use by a browser or for post-processing via
scripts. 

The full potential of annotated data is unleashed in combination with databases.
This was pointed by JMC. When I did my PhD in Erlangen, we had our own,
non-public archives for ab initio results (it still exists). This database
just stored data from different, often unrelated projects. But now imagine a 
dedicated database with computed structures (e.g. potentials inhibitors of an
enzyme). Tim Clark's group, as far as I know, has already done such a 
feasibility study of a such a "virtual" database. 
(Apologies to all of you working on similar projects but who I did not mention.) 
In short: I think there is consensus among chemists about the usefulness of and 
the need for annotated data; may it be in xml or any other format.

Amicalement,
Christoph