[Biodevelopers] RDBMS and Bioinformatics

Tue Mar 16 13:04:44 EST 2004

I think some types of data are better represented by XML.  For example,
hierarchical data.  Also, document-oriented data is better stored as XML.
For example, a scientific article that has been marked up with useful
information.  Storing and indexing something like "<Author>John
Doe</Author> used a <ScientificTechnique>microarray</ScientificTechnique>
to do blah" would be very complicated in a relational database.

Am I wrong?

-Patrick McConnell
Duke Binformatics Shared Resource
Duke Comprehensive Cancer Center
patrick.mcconnell at duke.edu

                      Dan Bolser                                                                                                                 
                      <dmb at mrc-dunn.cam.ac.uk>           To:       biodevelopers at bioinformatics.org                                              
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                      biodevelopers-admin at bioinfo        Subject:  Re: [Biodevelopers] RDBMS and Bioinformatics                                  
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                      03/16/2004 01:01 PM                                                                                                        
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                      biodevelopers                                                                                                              

On Tue, 16 Mar 2004, Michel Dumontier wrote:

> >
> > Same goes for BIND, they plan to use RDB, but not in a conventional way
> > (so far as I understand).
> >
>
>
> BIND (http://bind.ca) stores bind-objects based on ASN.1 specification
> (ftp://ftp.blueprint.org/pub/BIND/spec/, also available as XML DTD and
> Schema), as ASN.1/XML in BLOB fields in the database table.  BIND makes
use
> of field-specific indexing to be able to search for any particular object
or
> set of objects that match the search criteria.  The relational aspect is
> really more for curatorial work and tracking, afaik...

So it wont be like an XML query system? Sorry if I misunderstand, but it
sounds like you just do plain text index on an XML blob, but is is more
than that?

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?

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
>
>
>
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