[Pipet Devel] Re: XML

[J.W. Bizzaro]

Guy Hulbert wrote:
> 
> Previously visual genomics had some restrictions on use of BSML.  They still
> regard this as their intellectual property.  See:
>         http://www.visualgenomics.com/bsml/index.html
> for their current ideas.  I don't think this is suitable for a "GNU project".

Agreed.  We have no intention of doing a cut-and-paste of any "proprietary XML"
like BSML or BioML.  We only wish to judge the approaches taken and see if we
could do better.  Besides, there really is no patent on BSML or BioML, and it
would seem odd trying to close-source an XML, especially when they post the
DTD's on the Web sites.


> I don't like either BioML or BSML.  It seems to me that they are much too
> large --- trying to provide a complete 'bio-html'.   With XML namespaces
>       [ see:  http://www.xml.com/xml/pub/1999/01/namespaces.html ]
> one ought to be able to to put together small DTDs for specialized data.

I agree with you 100%!  Biological information is (1) too large, (2) too
complex, (3) changes too frequently, and (4) is incomplete--much is still
unknown.  This would make for an enormous moving target for any one DTD.

PLUS, there is a mistaken notion with BSML and BioML that bioinformatics ==
sequence information.  What about structure???


> and with approiate style sheets, Mozilla and Internet Expoit^H^Hrer
> would be able to display them.

It seems the Web browser is trying to become a universal GUI.  Either we
surrender the desktop and OS to Netscape and MICROS~1, and have everything run
through one window, or we continue to make applications with a limited set of
functions but that are able to do what they do very well.

> I'm keen to work with anyone on getting these small things set up.  As
> an experiment,  I'm planning to play with the Genbank data to create the
> basic facility to create documents like the above.

GenBank translation is probably the first translation project for Loci.  We
(myself and a few others working on Loci) would love to help.


:-)
Jeff
-- 
J.W. Bizzaro                  mailto:bizzaro at bc.edu
Boston College Chemistry      http://www.uml.edu/Dept/Chem/Bizzaro/
--