Bioperl: XML

[Paul Gordon]

> The BioPerl list hasn't mentioned XML since January... The message below
> was forwarded to me.  What is the current view/status in the BioPerl
> community as regards XML?  There was talk of a BoulderIO <-> XML convertros
> as well as a CGI <-> XML converter.

If anyone is interested, I'm working on and off (though unfortunately more
off than on) on a system for converting various biopolymer sequence
database entries into XML, with a Java viewer of the results.  I've
written a Perl BIOML generator class, and converters for Swissprot and
Genbank entries.  Note that this is all very *prelimenary*.  When I
actually get the code in good shape I could make it available for others
to use and add onto.  I use the Perl to convert pages from native format
into BIOML on the fly a la Lincoln Stein's Adblocker proxy, but the
conversion classes could certainly be used for other applications.  If
BioPerlers are interested in using BIOML, this could be a start.

For those who are interested, a very first, very rough (so don't
complain!), demo of Bluejay is available at

http://maggie.cbr.nrc.ca/bluejay

For a full fledged BIOML browser (for Windows) look at Ron Beavis' work

http://www.proteometrics.com/BIOML


	Paul Gordon
	Genomic Technologies
	Institute for Marine Biosciences
	National Research Council of Canada


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