[BioSQL-l] Description

[Chris Fields]

D'oh, it's in the README!

....

This is the BioSQL distribution. BioSQL is a generic unifying schema
for storing sequences from different sources, for instance Genbank or
Swissprot.

BioSQL is meant to be a common data storage layer supported by all the
different Bio* projects, Bioperl, Biojava, Biopython, and Bioruby.
Entries stored through an application written in, say, Bioperl could
be retrieved by another written in Biojava.

chris

On Sep 11, 2007, at 10:10 AM, Chris Fields wrote:

> 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
>
>
>
> _______________________________________________
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> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

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