[BioSQL-l] redundant qualifier values & Bio::SeqFeature::SimilarityPair

[Daniel Lang]

Thanks, Hilmar for the fast answer...
My error! You were perfectly right!


But my second questions still remains:
 >> Additionally I´d like to know if there is an adapter or a way to
 >> store  Bio::SeqFeature::SimilarityPair s in the schema yet?


Daniel:)



Hilmar Lapp wrote:
> Without any investigation into when this is actually happening, what I  
> can tell you is that this sort of duplication is not supposed on happen  
> when you create (insert) a fresh sequence into the database. Try to  
> check whether this is what is happening in your situation (I doubt it).
> 
> The situation when this would happen naturally is when you update a  
> previously looked up sequence after you merged it with new annotation  
> and didn't carefully reconcile the new annotation with the existing one  
> to avoid any duplication. This reconciliation step is non-trivial, as  
> it requires you to make some decisions (is an annotation that is on the  
> existing but not on the new sequence record stale [to be removed] or  
> non-public [to be kept]), and to find a good measure of when two  
> annotations are identical.
> 
> I believe the merge function examples that come with bioperl-db will  
> attempt to reconcile annotations for bioentries, but probably not for  
> their features (BTW updating features themselves suffers from the same  
> problem). I'd have to check, but that's my guess.
> 
>     -hilmar

-- 

Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang at biologie.uni-freiburg.de

#################################################
 >REALITY.SYS corrupted: Reboot universe? (Y/N/A)
#################################################

Join MOSS 2004 in Freiburg, Germany from September 12th - 15th:
registration and information @ http://www.plant-biotech.net/moss2004