[Biodevelopers] RDBMS and Bioinformatics

[Dan Bolser]

On Tue, 13 Apr 2004, Marc Dumontier wrote:

> Dan Bolser wrote:
> >
> >OK, final question, how will you do complex queries across the data?
> >
> 
> We use Lucene (http://jakarta.apache.org/lucene) to make a 
> field-specific text index. This software package provides us with a 
> query language which is very robust; all we have to do is tell it how to 
> index our data....the rest is done for us.
> 

I was thinking more along the lines of data integration. I know you have
ASN.1 underneath the data and ASN.1 <-> XML mapping is transparent, but
suppose some new data comes along and you want to query across this too.

I guess this is a problem for any system.

Is there nothing you can't do with Lucene that you can do with SQL? - How
about aggrigate functions?

Cheers,
Dan.


> 
> Marc Dumontier
> 
> >>Marc Dumontier
> >>
> >>    
> >>
> >>> 
> >>>
> >>>      
> >>>
> >>>>we should be releasing a beta of this software in a short while...please 
> >>>>visit http://www.bind.ca periodically for more information.
> >>>>
> >>>>Marc Dumontier
> >>>>BIND Software Developer
> >>>>Blueprint Initiative
> >>>>Mt. Sinai Hospital
> >>>>Toronto,ON
> >>>>
> >>>>Dan Bolser wrote:
> >>>>
> >>>>   
> >>>>
> >>>>        
> >>>>
> >>>>>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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> >>>>>>  
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>            
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> >>>>>
> >>>>>     
> >>>>>
> >>>>>          
> >>>>>
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