[Pipet Devel] BioML vs BSML

david.lapointe at umassmed.edu david.lapointe at umassmed.edu
Sun Jan 24 13:01:56 EST 1999


There is a Perl-XML FAQ at http://www.perlxml.com/faq/perl-xml-faq.html

Also, Activestate.com has a bunch of perl mail-lists running, one of which
is the PERL-XML list (http://www.activestate.com/lyris/lyris.pl). You can
browse the archives as a guest. CPAN has several XML related modules.

http://www.perl.com/CPAN/modules/by-category/15_World_Wide_Web_HTML_HTTP_CGI
/XML/


David
> -----Original Message-----
> From: Harry Mangalam [mailto:hjm at cx408397-a.irvn1.occa.home.com]
> Sent: Sunday, January 24, 1999 12:38 AM
> To: tulip-list at busboy.sped.ukans.edu
> Subject: Re: [Pipet Devel] BioML vs BSML
>
>
> Hi Jeff et al,
>
> As you probably have found out now, BioML is being used by
> the bio.perl
> group and the perl masters at perl.org already have a pretty
> large archive of
> useful scripts for manipulating XML.
>
> And it looks like, in a VERY fast spin thru the docs, that
> using their XML
> parser tools, it may be possible to use both of these XMLs,
> using these perl
> modules to handle parsing and interconversion.
>
> ie:
> http://www.perl.com/pace/pub/perldocs/1998/11/xml.html
> http://www.perl.com/pace/pub/perldocs/1998/12/cooper-01.html
>
> perl also has gtk bindings and in general, I've heard about
> and done more
> things using perl in the bio world than with python.  Not to
> say python
> doesn't make some or even most things easier - just that perl
> has a proven
> track record in the bio area.
>
> It seems not to be at cross purposes to the objectives of
> LOCI to implement
> chunks of it in perl, no?  As long as it remains easliy
> implementable, and
> usable, and freely re-distributable, perl is as much of an option as
> python, isn't it?
>
> Also, how is the LOCI project planning on handling the display of the
> results of this effort?  Both the BioML and the BSML browsers that are
> available are MS-centric and certainly do not use gtk.  The
> only browser
> that I'm aware of that does is gzilla (www.gzilla.com) and mnemonic (
> http://www.mnemonic.org/).  Are you planning on using either
> of these for
> your display dev platform?  Or are you not implementing any display
> technology?
>
> VisualGenomics is planning a Java-based BSML browser, but I'm
> sure that it
> won't use gtk, unless heavily funded.  It'll probably be
> written with the
> swing classes - what's the redist controls on swing - I'm not a Java
> follower - sorry.
>
> OK - enough mind rot from me for the present...
>
> Cheers
> harry
>
> On Sat, 23 Jan 1999, J.W. Bizzaro wrote:
>
> > Harry,
> >
> > We had some rather lengthy exchanges about the use of BSML
> and CML in Loci.  We
> > were looking for an XML that would work well for both
> sequence and structure
> > information.  But it seemed that neither was good at both.
> >
> > In sort, we stepped back from the issue, and decided we
> would try to support
> > BOTH, until something better came along.  We even
> considered making our own XML
> > (we would call it BMML, "BioMolecule Markup Language").
> What we really wanted
> > was just one language that would give us an excellent
> description of large bio
> > macromolecules.  Well, of course that would have been too
> much to take on right
> > now.
> >
> > Konrad actually has a lot to say about descriptive
> languages for macromolecule
> > structure.  He had corresponded with Peter Murray Rust, the
> author of CML and
> > someone rather influential in the development of XML.
> Konrad, as he can tell
> > you, is not satisfied with any current format.
> >
> > BioML comes as a bit of a surprise to me.  It seems to be
> brand new.  Looking it
> > over a bit, it does seem to do a better job at handling
> structure than BSML, and
> > I like the inclusion of all sorts of biological information
> (it can describe
> > organisms as well, it seems)...although some may argue this
> is "bloat".
> >
> > I would like Konrad to give us his impression of BioML.  It
> would be nice to use
> > one XML rather than two.  My big question, however, is the
> licensing.  The Web
> > page says to contact David Fenyo about the "commercial" use
> of BioML.  I wonder
> > if this is one of those "well, as long as you don't make
> money on it" licenses.
> > If so, we have problems: It won't fit with GNU GPL.
> >
> > I wrote a message to David Fenyo about this, and to see if
> he can give us a
> > contrast between BioML and BSML.  A cc will be sent to the
> Tulip list.
> >
> >
> > Cheers!
> > Jeff
> > bizzaro at bc.edu
> >
> >
> > Harry Mangalam wrote:
> > >
> > > Hi All,
> > >
> > >    Having only recently come to this arena, what's the
> group's evaluation of
> > > the relative merits of BSML:
> > > http://www.visualgenomics.com/sbir/rfc.htm
> > >
> > > vs BioML:
> > > http://www.proteometrics.com/BIOML/
> > >
> > > I'm still going thru the text of the specs but if any of
> you have strong
> > > arguments regarding either approaches, I'd very much
> appreciate it.  The
> > > bioperl people seem to like the BioML approach.
> > >
> > > Also, if you have come to an approach that can
> rationalize the competing
> > > stds, please let me know.
> > >
> > > Cheers
> > > Harry
> >
> > --
> > J.W. Bizzaro                  Phone: 617-552-3905
> > Boston College                mailto:bizzaro at bc.edu
> > Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/
> > --
> >
>
> Cheers,
> Harry
>
> Harry J Mangalam, Developmental + Cell Biology
> Rm 4201, Biological Sciences II, UC Irvine, Irvine, CA, 92697
> (949) 824 4824[vox], (949) 824 8551[fax], mangalam at uci.edu
> http://hornet.bio.uci.edu/~hjm/
>



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