[BioSQL-l] Description

[Chris Fields]

Here's a question I couldn't find the answer to: should any BioSQL- 
loaded data (via BioJava, BioPerl, etc) be expected to fully round  
trip across any BioSQL-utilizing language?  In other words, if I use  
BioJava/Hibernate to load sequence data in to a BioSQL database and  
use BioPerl to work with the data, can one expect it to work?

My guess is no, as long as there is no formal specification...

chris

On Sep 11, 2007, at 9:54 AM, Richard Holland wrote:

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> There is no formal specification for what goes where in BioSQL, but  
> you
> can refer to the BioJava documentation for a good approximation of  
> where
> a GenBank file should end up. The BioJava objects share similar  
> names to
> the BioSQL tables and are mapped using Hibernate.
>
> The most useful parts of the docs are probably:
>
> http://biojava.org/wiki/BioJava:BioJavaXDocs#GenBank
>
> and:
>
> http://biojava.org/wiki/BioJava:BioJavaXDocs#Hibernate_object- 
> relational_mappings.
>
> cheers,
> Richard
>
> Paul Davis wrote:
>> I've been going over the biosql schema and I was wondering if there
>> was a good place to read about examples of actual data that goes into
>> each table. Specifically, I'm a bit confused about which parts of a
>> genbank record go in which tables.
>>
>> Thanks,
>> Paul Davis
>> _______________________________________________
>> BioSQL-l mailing list
>> BioSQL-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biosql-l
>>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign