[Bioperl-l] biosql and relationships

Hilmar Lapp hlapp at gmx.net
Mon Aug 2 08:28:53 EDT 2004

The bioentry_relationship table is meant for exactly this purpose 

Since bioperl doesn't have a straightforward corresponding class, 
however, it is not supported through the bioperl object layer except 
for Bio::ClusterI objects (e.g., Bio::Cluster::Unigene).

There's different courses you could pursue. What I'm doing in my 
instance is making heavy use of SQL scripts that I run against the 
database on a regular basis, and which would synthesize those 
relationships based off of, for instance, dbxref-to-bioentry matches. 
Instead of running sql directly, you run also wrap a perl script around 
it for processing input files or things like iterative/recursive 
queries. Or you could amend bioperl (and then bioperl-db) to support 
this in a better fashion.


On Monday, August 2, 2004, at 12:05  PM, Sean Davis wrote:

> I have loaded a few databases for local use into a biosql database.  I 
> am interested in including bioentry_relationships between these 
> databases.  The information is typically included in the file (eg., 
> the locuslink id in the refseq record).  Is there a way to do this?  I 
> know this information is also stored in various dbxref tables, as 
> well, but wondered how the bioentry_relationship table is used, if it 
> is not for creating relationships between bioentries, even if they are 
> in separate namespaces.
> Thanks,
> Sean
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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