BioWidget meeting

[Steve A. Chervitz]

Georg Fuellen wrote:
> 
> SteveC wrote,
> > I very much agree. I have a number of examples of how I am using Perl 
> > and Java in precisely this manner. One of the big issues with the BioWidget 
> > folks is to avoid getting caught up in sematics. "Drive sematics out," they 
> > say (after David Searls). They want to create a semantically neutral system 
> > for displaying and manipulating graphically any kind of genomic data. But 
> > at some point you must deal with the semantics of biological objects 
> > (primarily, this is a data model issue, I believe). I think Perl is well 
> > suited to deal with semantic issues. This could be a good angle to present 
> > at the conference. For example, we could cast Perl as an intermediary 
> > between a semantically complex biological object and a semantically neutral 
> > Java bioWidget.  What do you think?
> 
> This looks exciting, but I'm not clear in which way the 
> ``semantically complex biological object'' is represented, so that Perl can
> act as an intermediary between this object and a Java bioWidget.

I'm not quite sure myself, but the basic idea would be to use a parallel 
object schema in both the Perl and Java to facilitate mapping between 
Perl and Java objects. 

> Also, am I right that ``semantically neutral'' means that a bioWidget
> can display any piece of data that conforms to a certain syntax, or ?

Yes. A bioWidget is expected to conform to an common API that allows
for various display tasks such as selection, highlighting, and coordinated 
scrolling/zooming. This permits a consistent interface across widgets. 
At some level, though, there has to be some semantic tie-in so that a 
specific bioWidget knows how handle the peculiarities of biological 
information from a specific domain. One could imagine there being 
subtypes of bioWidgets that specify more about the domain data which 
would act as a base class for all widgets of that type (e.g., 
SequenceWidget, MapWidget).

Check the bioWidget homepage for more about this:
http://goodman.jax.org/projects/biowidgets/consortium/

Regards,
SteveC