Subject: Re: CCL:XML for Bioinformtics Data

From: Konrad Hinsen <[email-masked]>
Date: Fri, 30 Apr 1999 15:01:25 +0200

> XML. Some work in this area has already been done. For more
> information on the Biosequence Markup Language (BSML)
> see the WWW page of Visual Genomics Inc. at
> 
>     http://www.visualgenomics.com/bsml/index.html
> 
> A BSML browser and examples are available for download.

And that's not the only one, see for example BioML
(http://www.proteometrics.com/BIOML/). It remains to be seen if any
proposed DTD will gain acceptance; I wouldn't be surprised if the
"first generation" DTDs turned out to be insufficient at a later time.

> What is not currently clear to me is whether a given markup language
> must to be approved by the WWW consortium,  the Math markup
> language 1.0 (http://www.w3.org/Math/) has been released as
> a W3C recommendation. in April 98; but is this required ?

No. You don't even have to tell anyone that you are using a particular
DTD (Document Type Definition, i.e. the definition of a particular XML
or SGML application). MathML is designed by the W3C, but anyone else
can freely use XML for any other purpose.

I agree that XML holds a lot of promise for all branches of scientific
computing, where people waste incredible amounts of time due to badly
designed, undocumented, and incompatible file formats. However, XML
only helps, but doesn't guarantee success. Another problem is that XML
requires rather sophisticated processing, which makes it improbable
that legacy Fortran programs will ever be able to handle it. Newly
designed programs can of course profit from existing XML tools and
libraries.

Even the worst possible XML scenario (lots of similar but incompatible
DTDs used in different programs) will be better than the current
format chaos, because at least the syntax will be standardized and the
semantics can often be guessed reliably. So don't wait, start using
XML now!
-- 
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Konrad Hinsen                            | E-Mail: [email-masked]
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