[Biojava-l] Should we standardise on an XSLT processor?

Juha Muilu muilu@ebi.ac.uk
Mon, 11 Dec 2000 19:37:35 +0000

Simon Brocklehurst wrote:
> "Dickson, Mike" wrote:
> > 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.
> An XSLT transform for converting between formats is certainly what we had in
> mind (but we haven't really looked in detail yet to see how much of a pain this
> will be).    Also, we've been holding off putting any XSLT stuff into biojava
> thus far because mechansims for adding Java extensions to XSL stylesheets aren't
> standardised.  It turns out that, for bioinformatics stuff, building Java
> extensions to XSL seems to be pretty much the rule rather than the exception.
> At CAT, we currently use Saxon as our default XSLT processor.  The reason for
> making this choice over Xalan is that Saxon was the more robust/reliable of the
> two when we made the choice.  I have no idea whether Xalan is currently robust -
> it may well be. Does anyone out there have strong feelings about using Xalan
> rather than Saxon, or substantial experience with latest versions of both?
> Would people out there be happy to standardise on Saxon, and thus the Saxon
> method for writing Java node handlers for the time being?

It would be interesting to know how different XSLT implementations
especially with large data files. Memory usage may be a problem if all 
data is kept in memory during the transformation. Especially when the
XML tree  
etc. can easily eat over a magnitude more memory than original data..


> 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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 |Juha Muilu, Ph.D., EMBL Outstation| Email:  muilu@ebi.ac.uk         |
 |European Bioinformatics Institute | Phone:  +44 (0)1223 494 624     |
 |Wellcome Trust Genome Campus      | Fax:    +44 (0)1223 494 468     |
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