[Biodevelopers] RDBMS and Bioinformatics

[Dan Bolser]

On Tue, 16 Mar 2004, Patrick McConnell wrote:

> 
> 
> 
> 
> 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?

No, of course you are not wrong, but the thing is that you could do the
above in an RDB, and (if you do it right) the data model is very clear,
the data is normal it is easy to search and integrate, easy to make tab
delimited dumps of, and best of all you have internal constraints on the
data. The query system is (or can be) optimal, because of the sound maths
underneath. I still agree with your point though...

The idea of markup is truely powerfull. I had forgotten that XML is a
markup language! You are absolutely right that documents don't fit RDB
well. Also, while hierarchical data is very easy and just as flexible, XML
is more intuativly hierarchical, while RDB stores an abstract hierarchy
which is not easy to query.

Still, I would be more in favour of developing hierarchical indexes for
SQL to allow better querying features (i.e. an sql native tree data
type?), and semantic markup languages like DAML, while never using XML
object models / object DB / X-pah etc.

Cheers,
Dan.

> 
> -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                                              
>                       Sent by:                           cc:                                                                                     
>                       biodevelopers-admin at bioinfo        Subject:  Re: [Biodevelopers] RDBMS and Bioinformatics                                  
>                       rmatics.org                                                                                                                
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>                       03/16/2004 01:01 PM                                                                                                        
>                       Please respond to                                                                                                          
>                       biodevelopers                                                                                                              
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> 
> 
> 
> 
> 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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