[Pipet Devel] BioML vs BSML

[J.W. Bizzaro]

Konrad Hinsen wrote:

> I don't think my opinion is so relevant; my field of work is rather
> different from the Loci project. I work on structures

Are you kidding?  Half of loci will be for structural analyses!  People think
bioinformatics is just about sequence analyses, and I believe wrongly so. 
Because many people exclude structural analyses, we were careful to name The BIC
Group, "The Biomolecular Informatics and Computation Group".  So we are involved
in informatics plus anything else that involves computers and biology.

I want to make certain that we include structural analysis tools in our list of
analysis tools to be used.

> and BioML
> does not seem to have any provision for structures at all. Which is
> fine, of course, not everything has to be designed for my needs ;-)

I recall some BioML examples with structural data.  Unless your talking about
BSML.  But you'll say that including structural data and making a good provision
for it are completely different ;-)

> I am not even sure that a data format is copyrightable. If it is, the
> current downloadable DTD does not contain any copyright statement or
> usage restrictions, so I don't see why it shouldn't be used for
> commercial applications.

Hmmm.  And we didn't hear back from them.

> That aside, I did notice a couple of strange features in and about
> BioML that make me wonder whether it is the format of choice. First,
> and most importantly, I have the impression that the inventors have
> not quite understood the point of XML - separating content from
> layout. BioML contains some purely graphical entity definitions, for
> example &paragraph; defined as &newline;&tab;. In my opinion such
> things should never appear in XML files. Paragraphs should be marked
> up with a paragraph tag, whose visual interpretation is left to a
> stylesheet definition.

That is strange and maybe a good reason to not use it.

> Second, the BioML inventors seem to be more Windows-centric than
> Microsoft itself. Who would have the crazy idea of offering
> documentation in portable HTML format only as a self-extracting
> archive for Windows? Of course this doesn't affect the language,
> but I'd hate to see the next release contain tags for defining
> COM objects...

Windows is the world...not.


Jeff
-- 
J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/
--