[Bioperl-l] xml standard for sequences

[Paul Gordon]

The short answer, is that there is no standard.  The problem is that
most people want to include their own set of tags, such as annotation, on
top of the base information about the sequence.  And everyone has a
different idea of what that extra info should be.  Check out my slightly
out of date page (I swear I'll work on it! :-))

http://maggie.cbr.nrc.ca/~gordonp/xml/

and you'll see the diversity.  It too bad bioxml.org died, it could be a
discussion and DTD (much needed!) repository for the community, instead of
trying to come up with a common syntax.  Is their anyone still at the
reigns there?  If you're looking for Perl compatibility, I think you're
best off looking into BSML or DAS.

My CAN$ 0.02

----------------------------------------------------
Purgamentum init, exit purgamentum

Paul Gordon
Research Associate
University of Calgary

On Tue, 16 Apr 2002, Gila Lithwick wrote:

> Hello,
> I want to start working with XML, and would like to use the standard
> dtds for sequence data (if they exist).
> I noticed that bioxml no longer exists, that EBI creates XML files for
> protein data, that ncbi has a parser for its asn files, and that a
> couple companies have there own dtds (Bioml, bsml).
> Is there a dtd that's supposed to be the standard for sequence (dna and
> protein) data?
> (And what happened to bioxml?)
> Thanks,
> Gila.
> 
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