[Bioperl-l] xml standard for sequences

[Brian King]

Hi Gila,

Like everyone has said, there is no standard sequence
XML format, but AGAVE is an open source format
available for your use.  I'm maintaining AGAVE at

http://www.animorphics.net/lifesci.html

The AGAVE 2.3 DTD is there, and for those interested
in schemas I created a 3.0 version in schema form that
improves on the 2.3 design.  

Currently you can get EBI data in AGAVE format at
http://www.ebi.ac.uk/xembl/.  The XEMBL server does
the EBI to AGAVE conversion using BioPerl modules.

Best Regards,
Brian King

 
------------------------------------------------ 
 
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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