[Bioperl-l] Database Retrieval

Chris Fields cjfields at uiuc.edu
Mon Aug 7 13:13:18 EDT 2006

On Aug 7, 2006, at 11:54 AM, Sean Davis wrote:

> On 8/7/06 12:24 PM, "Chris Fields" <cjfields at uiuc.edu> wrote:
>> This was brought up previously:
>> http://article.gmane.org/gmane.comp.lang.perl.bio.general/11808/
>> match=ucsc
>> Would be nice to get something up and running here, even if it just
>> returned raw data (not objects).  The more access the better.
> Sorry, Chris.  I probably sound like a broken record--UCSC, UCSC,  
> UCSC....

Never hurts to reiterate here.  Well, to a certain degree...

> As I hinted at in the last email, simple Rose::DB::Object (my  
> preference,
> faster) or DBIx::Class based classes could be set up for the  
> various tables
> of interest, with the possibility of adding functionality by simply  
> adding
> methods to the generic ORM classes.  This would be relatively quick to
> develop I would think and pretty easy to maintain.  If I get a  
> chance in the
> next few days, I can put together a quick set of classes for  
> accessing some
> of the common tables.
> Sean

I guess these could go under the Bio::DB* namespace unless someone  
disagrees.  I don't think it's absolutely necessary get any raw data  
into bioperlish objects immediately.   Just setting up access to UCSC  
would be a great start, and the classes could evolve from there to  
slowly get 'assimilated' into Bioperl.  Hmm... makes Bioperl sound  
like the Borg...

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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