[Bioperl-l] xml standard for sequences

Brian King kingb_98@yahoo.com
Tue, 16 Apr 2002 12:00:07 -0700 (PDT)


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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