Bioperl: XML/BioPerl - design proposal

[David J. States]

-----Original Message-----
From:	Wayne Parrott [SMTP:wayne@workingobjects.com]
...One of the recent post in this thread caught my attention. It
was regarding a plan to transform application output into XML, such as
Blast. I agree this is the way to go. But before "just going and doing
it" allow me to propose a design model for consideration....

The discussion of frameworks and design patterns is interesting but under 
emphasizes a critical point, which is the need to develop and maintain 
standards.  We have a reasonable proposal for sequence XML definition, 
BIOML, as well has a highly developed set of ASN.1 definitions developed 
that NCBI and widely used flatfile definitions for GenBank and 
EMBL/Swissprot.  The NCBI definitions include sequence alignment as well a 
sequence definitions.  Finally, bioperl itself has a well developed set of 
sequence and alignment structures.  To be useful to the community, a new 
set of JAVA tools must support the existing data standards or least provide 
a straightforward way of mapping from existing standards to the standards 
used by the tools.  In all the frameworks discussion, I did not see much 
mention of this.

David States

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