[Biojava-l] Preparation for a 1.1 release?

[Dickson, Mike]

Your approach would certainly be my preference.  There is an unfortunate
proliferation of specialized XML formats being developed.  A more normalized
view that can represent concepts generally makes more sense to me.  Perhaps
an XSL style sheet that can map from the NCBI format into the more general
biojava format would be beneficial.

Mike

> -----Original Message-----
> From: Simon Brocklehurst
> [mailto:simon.brocklehurst@cambridgeantibody.com]
> Sent: Monday, December 11, 2000 4:48 AM
> To: uwe.plikat@pharma.novartis.com
> Cc: biojava-l@biojava.org
> Subject: Re: [Biojava-l] Preparation for a 1.1 release?
> 
> 
> uwe.plikat@pharma.Novartis.com wrote:
> 
> > Hi Thomas,
> >
> > reading "Blast parsers" and hearing Matthews presentation 
> last week at EBI,
> > I just want to make one comment:
> > Matthew mentioned a Blast2XML parser. Since Blast by itself 
> can produce XML
> > output (option -m7) it would be a good idea, if this parser (kind of
> > obsolete...) produces the XML format identical to the 
> original one from
> > NCBI. The DTD is available at NCBI's ftp site.
> 
> Hi Uwe,
> 
> One of the points of the XML format for the biojava 
> Blast-like stuff is that it
> doesn't actually revolve around NCBI Blast.  That is, it can 
> represent data
> output from WU-Blast and Hmmer as well.  The biojava XML 
> format is also
> designed to be invariant with respect to different versions 
> of all these
> programs (once it goes into a full biojava release).  I think 
> it remains to be
> seen whether or not the NCBI DTD remains stable, or is 
> subject to change
> without notice or reference to users in upcoming versions of Blast.
> 
> I don't think we have yet put enough code into biojava yet, 
> to demonstrate the
> utility of taking this approach.  Having said all that, we 
> are hoping to make
> everything work smoothly and seamlessly with the NCBI Blast 
> XML output.
> 
> Simon
> --
> Simon M. Brocklehurst, Ph.D.
> Head of Bioinformatics & Advanced IS
> Cambridge Antibody Technology
> The Science Park, Melbourn, Cambridgeshire, UK
> http://www.CambridgeAntibody.com/
> mailto:simon.brocklehurst@CambridgeAntibody.com
> 
> 
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