[BioSQL-l] DBXRef

[Matthew Pocock]

Hi Hilmar,

If DBXref is replaced with joins between entries, then we loose the 
ability to link from a biosql-serialized sequence to a remote sequence 
(e.g. from a biosql image of an embl entry to a web-service image of a 
swiss-prot entry). Or, imagine you have imported the muman division of 
embl into biosql, how would you represent links to the non-human 
entries? Perhaps both mechanisms could be used, butg then we are 
providing multiple ways to represent the same information. Mmm. Don't know.

Matthew

Hilmar Lapp wrote:
> I propose to convert the implicit foreign keys to bioentries captured as 
> DBXref into explicit foreign keys to Bioentry.
> 
> This enables integrity checking by the database, fast and simple joins, 
> and provides for easy annotation/decoration of DBXrefs (because they'd 
> become no less annotatable as any other Bioentry).
> 
> At the same time, this change would give rise to a Bioentry-Bioentry 
> association table, which we need anyway to represent relationships 
> between bioentries, one of the central concepts of the database we're 
> building here. These associations would be typed.
> 
> To extend this, eventually these relationships will also need to 
> reference evidence. If anyone has thoughts on this please share. This is 
> not our most immediate problem though.
> 
>     -hilmar
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
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