[Pipet Devel] BioML vs BSML

Konrad Hinsen hinsen at cnrs-orleans.fr
Mon Jan 25 05:11:54 EST 1999

> I would like Konrad to give us his impression of BioML. It would be

I don't think my opinion is so relevant; my field of work is rather
different from the Loci project. I work on structures, 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 ;-)
My complaint with CML is that it claims to handle biomolecular
structures and does it badly.

> 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,

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.

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.

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...

Konrad Hinsen                            | E-Mail: hinsen at cnrs-orleans.fr
Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-
Rue Charles Sadron                       | Fax:  +33-
45071 Orleans Cedex 2                    | Deutsch/Esperanto/English/
France                                   | Nederlands/Francais

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