[BioSQL-l] (no subject)

[Hilmar Lapp]

Yes indeed. The only thing I would add is that BioSQL at present  
doesn't encompass structures, so if you also want to store the PDB  
structures you will have to have your own way of doing this.

(That is not to say that BioSQL couldn't start storing structures as  
well. I haven't really worked with protein structures though, so at a  
minimum someone else would have to drive that.)

	-hilmar

On Jul 21, 2008, at 11:00 AM, James Procter wrote:

> Hi Jay.
>
> Jay Vyas wrote:
>> H Hilmer  :  Where is the data for BIO SQL ?  Is there a single non
>> redundant PDB database which is in Bio SQL format?  Thanks !  Jay
> ...
> BioSQL is a standardised database schema for storing sequence and
> metadata, rather than a format for distributing sequence and  
> annotation
> data.
>
> I'm not sure if any of the public bioinformatic database repositories
> serve BioSQL dumps of their data, but it sounds like it might be a  
> good
> idea :)  However, since both BioJava and BioPerl have routines for
> transparently mapping between Java or Perl objects and the sequences  
> and
> annotation in any BioSQL database - so its pretty easy for you to  
> make a
> version of the PDB NR yourself.
>
> hope it helps
> Jim
>
> -- 
> -------------------------------------------------------------------
> J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No.  
> SC015096.
>
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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