[BioSQL-l] Description

[Hilmar Lapp]

On Sep 11, 2007, at 10:54 AM, Richard Holland wrote:

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> There is no formal specification for what goes where in BioSQL,

Indeed there isn't a formal specification in text. To understand this  
it may be worth keeping in mind that the historic, and still in a  
sense primary, use-case of BioSQL is to be the common persistence API  
for the Bio* projects.

Hence, what is relatively well defined is how to map a Bio* object  
model (in particular, BioPerl's - and meanwhile Biojava's - object  
model) into BioSQL and back. Where a particular piece of a GenBank  
file ends up in BioSQL would therefore depend on where it ends up in  
the respective object model, strictly speaking.

Since this doesn't bode well for interoperability between the  
toolkits (which was one of the points of having BioSQL) Richard, Mark  
Schreiber, and I got together 2 years ago to reconcile BioPerl's and  
Biojava's way of ingesting and representing a richly annotated  
sequence, leading to the RichSeq work being added to Biojava (correct  
me Richard if I'm confusing things).

So in theory, at least meanwhile BioPerl and Biojava should map a  
GenBank sequence to BioSQL in a very similar or ideally identical  
way, so I'm not sure this has ever been put to the test.

I'm not aware of a similar effort that has been undertaken on the end  
of Biopython, though I'd be more than happy to work with anyone from  
the Biopython community who is interested in resolving this. Given  
the recent Bio.SeqIO work there, this may be a good time to take this  
up.

	-hilmar

> 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

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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