[Biodevelopers] RDBMS and Bioinformatics

[Joe Landman]

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.

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).  

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
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.

They generally solve different problems, though there is overlap.  

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

:)

> 
> 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
> > 
> > 
> > 
> > _______________________________________________
> > Biodevelopers mailing list
> > Biodevelopers at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/biodevelopers
> > 
> 
> _______________________________________________
> Biodevelopers mailing list
> Biodevelopers at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biodevelopers