[Biodevelopers] RDBMS and Bioinformatics

[Joe Landman]

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.

GUT/TOE's and similar are attempts to push up against the limits.  At
some point they run into the problem that the method to describe the
theory (the underlying mathematics) is incomplete relative to what they
need.  When it comes to this, they extend the underlying mathematics
(sometimes to the chagrin of the Mathematicians).  Sometimes this works
spectacularly well (Newtons laws and calculus, though it is quite
debatable whether or not Newton was a mathematician working on applying
the math to natural philosophy, or a natural philosopher needing better
tools).  Other times not so well.

These are good efforts and theoretical physics is an excellent
user/builder of mathematical tools for its purposes (notwithstanding the
several grad students I used to bump into from Mathematics who grumbled
about existence proofs for solutions to various potential function
versions of the Schroedinger equation).

Of course, we have wandered OT here. 

> > > 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.

Joe