[BioSQL-l] BioSQL + Embl + Comments

[Hilmar Lapp]

Hi Raoul,

On Mar 10, 2008, at 4:54 PM, Raoul Jean Pierre Bonnal wrote:

> Dear Hilmar,
> I'm here for asking you some help.
>
> BioRuby guys chosen as example for round trip tests the sequence ID
> AJ224122; SV 3; linear; genomic DNA; STD; PLN; 3827 BP.
>
> I have problem with the references/comments informations.
> In biosql "comment" seems to be something generic not directly  
> binded to
> a reference.

Comment in BioSQL is a piece of annotation of type comment. The  
schema at present only allows you to attach those to bioentries, and  
in fact one particular comment can be assigned to only one bioentry  
(1:n relationship).

> If you look at the AJ224122's embl format a comment is
> connected with the reference.

You're referring to the following line, right?

RC   revised by [3]

> There is no problem with genbank because there is only a generic  
> comment
> and BioSQL works correctly in this case.
> So, how can I manage the problem with Embl ? I was thinking to add a
> column the "comment_id" to "bioentry_reference" as fk to "comment"  
> table
> in a way that a bioentry_reference can have more comments.

One question here is whether the comment is specific to the  
association of the reference with the bioentry, or to the reference  
in general.

The next thing to note is that the comment above is not just text, it  
actually establishes a relationship to another reference (or to  
another reference to bioentry association). So to really capture it  
you would want a typed link between bioentry_reference rows (in this  
case the relationship type would be 'revises' or 'revised by',  
depending on direction).

The question is whether this depth of modeling is needed or useful,  
aside from the fact that I'm pretty sure that none of the Bio*  
libraries supports it (but maybe they want to?).

So if not, I guess this goes back to the use-case of round-tripping?  
Maybe to satisfy that a bioentry_reference_qualifier table would  
suffice (assuming that the comment does apply rather to the reference/ 
bioentry association than directly to the reference).

>
> PS: I don't know if this stuff should be emailed to biosql list

Yes, I actually hadn't realized that you hadn't posted this to the  
list. Should have forwarded right away, sorry for sitting on it.

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