[BioSQL-l] Increasing value of rank in table seqfeature

[Hilmar Lapp]

Hi Gabrielle,

smallint can take values up to 65535 if unsigned. I can see that this  
can become a limitation if the bioentry to which the features belong  
is a whole chromosome.

Note that the uniqueness constraint is not on bioentry (sequence) and  
rank. Instead, it is on the combination of bioentry (sequence), type  
term, source term, and rank. I.e., at present, with the smallint  
constraint, you can't have more than 65535 features of the same type  
and from the same source for a particular sequence.

It's possible that the software you are using (Biojava?) increments  
the rank for every single feature, rather than resetting for each new  
combination of type and source. Is that what you are seeing?

	-hilmar

On Aug 29, 2008, at 8:36 AM, Gabrielle Doan wrote:

> Hi all,
> I have a BioSQL database which contains several chromosomes and  
> features. And now I would like to insert chromosome 2 with some  
> miRNA as a new feature. I meet the problem that in the table  
> seqfeature the entry rank just can store smallint(5) unsigned  
> values. As fare as I know each rank has to be unique. If you want to  
> store many information this value will be excess quickly. Isn't it  
> better to increase this value?
>
> It would be very nice if someone could comment my suggestion. Thanks  
> a lot.
>
> Cheers,
> Gabrielle
> _______________________________________________
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> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

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