[BioSQL-l] Description

[Barry Moore]

Well, the schema is the formal specification as to what goes where  
and as long as your BioJava and BioPerl DB interface plays by the  
rules of the schema, then yes you should be able to use both  
languages on the same database.  Of course the devil is in the  
details and since I've only worked with the BioPerl interface I don't  
know if that is in fact reality right now.  I think what Richard  
meant was there is not detailed human documentation about where each  
bit of a GenBank record goes into what table and column.  Paul, I  
think you will find this document to be what you are looking for - or  
at least as good as you'll get:  go to http://cvs.open-bio.org/cgi- 
bin/viewcvs/viewcvs.cgi/biosql-schema/doc/?cvsroot=biosql and look  
for schema-overview.txt.  There is also a ERD in pdf format which can  
help you get your head around the schema.  If you end up with  
specific questions about what's where, send another e-mail or just  
load some files and go exploring.

Barry

On Sep 11, 2007, at 9:10 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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