[Pipet Devel] BioML vs BSML

[J.W. Bizzaro]

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/
--