[Biodevelopers] RDBMS and Bioinformatics

[Dan Bolser]

On Tue, 16 Mar 2004, Joe Landman wrote:

> On Tue, 2004-03-16 at 13:01, Dan Bolser wrote:
> 
> > Generally, can anyone tell me  what is the point of XML schema when
> > relational schema have existed for years with well understood maths, query
> > language and theories of relational design? I understand XML as a
> > transport medium, but why make it the basis for your object model over the
> > RDB relational schema? Perhaps object orented datamodeling can do things
> > relational modeling can't, but at what cost? I hate sounding old, but what
> > was wrong with the RDB that we have to invent X-path and the like?
> 
> I think the real answer is long and complicated, so I will try for the
> fake, short, and pedagogical.  
> 
> RDBMS's are well designed for tabular data with simple data types, and
> well defined structures and well known or "easily" describable
> relationships between the entries.  They are great at representing
> knowledge and algorithms that can be mapped onto this paradigm.

OK
 
> For dynamic data structures, or deeply nested data structures which may
> not in fact have constant well defined structures, they (RDBMS) are
> painful at best.  Measures such as serialization are used to map complex
> objects to RDBMS's, making use of the data within the serialized object
> hard to query (you have to de-serialize to search within it).  

Sure 

> Basically the object<->relational mapping is on one-to-one and onto in
> most cases, so you have to resort to "hacks" like serialization to make

Sorry, do you mean 'is not 1 to 1' ?

> sure information and state are not lost (my apologies to those who do
> not consider serialization to be a hack).  Objects can be rich and
> dynamic data structures which can be represented by an XML document to a
> degree (apart from the code elements), and can better represent dynamic
> data.

I follow. I guess it is rare that people make large amounts of data
available via XML (i.e. using XML as a database). The way you describe
sounds like a good use of XML - giving / transporting data about a
programs internal state.

> They generally solve different problems, though there is overlap.  

I am still a bit confused. I can't help thinking of dia, which makes
exelent use of XML to represent diagrams, and so has easy interchange with
lots of tools - i.e. good use of XML, it woudl be crazy to run dia off an
RDB. 

But what is the point in creating biological data in this form, when the
'data model' is basically our own concept about the data?

Wouldn't a SwissProt RDB be much more sensible than an XML document?

I get the feeling that I just don't get something. Basically my question
is this, if we invest time and effort in making a stable model of the
data, why not use RDB?

> 
> > Anyone on the list remember when relational databases were 'the new
> > thing'?
> 
> :)

Did people moan about them? ;)

Cheers
Dan.

> 
> > 
> > Dan.
> > 
> > > 
> > > Michel Dumontier
> > > PhD Candidate
> > > Samuel Lunenfeld Research Institute, Mt. Sinai Hospital
> > > Department of Biochemistry, University of Toronto
> > > Toronto, ON M5G1X5
> > > micheld at mshri.on.ca
> > > http://blueprint.org
> > > 
> > > 
> > > 
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