Re: RDBMS and Bioinformatics

On Thu, 18 Mar 2004, Joe Landman wrote:

> On Thu, 2004-03-18 at 04:46, Dan Bolser wrote:
> 
> > > > But what is the point in creating biological data in this form, when the
> > > > 'data model' is basically our own concept about the data?
> > > 
> > > One of these days someone is going to extend Go"del's incompleteness
> > > proof for biological systems. 
> > 
> > 
> > I wish someone would tell the physicists about it :) every time I see a
> > show about GUT I think Godel must be hopping mad!
> 
> :)  Careful, you might be speaking to one right now, and not even know
> it.

But are GUT's impossible according to Godel? That working on a GUT is a
waste of time or not is a different question. I take your point that the
activity alone can be very usefull without hope of sucess (like the search
for the philosophers stone).

 
> 
> Of course, we have wandered OT here. 

;) sci.physics.research ?

 
> > > > Wouldn't a SwissProt RDB be much more sensible than an XML document?
> > > 
> > > Only if the Swissprot never changes format.  The whole point of XML is
> > > the "X".  Extensible.  If you want to integrate portions of Swissprot
> > > into your own research DB, you can do this, but you would either have to
> > > deal with the Swissprot normalization model, or datamart the swissprot
> > > and create your own normalization .
> > 
> > 
> > Sure, but you have to understand the structure of the XML document just as
> > much as you would need to understand the data model of the RDB. Data
> > models do change, and you have to change code. Are you saying that
> > changing the structure of XML has less impact on the whole system? I guess
> > this is *the* reason people talk about XML.
> 
> Basically.  Once you have a parser for XML, it should (if it is working
> properly) parse *any* XML.  So your structure can change, or your
> information can change without altering your code for the most part.

Well, I will take your word for it! 

Cheers,
Dan.


> 
> Joe
> 
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