[Bioperl-l] biosql and relationships

Robson Francisco de Souza {S} rfsouza at citri.iq.usp.br
Tue Aug 3 22:40:07 EDT 2004

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

On Mon, Aug 02, 2004 at 01:28:53PM +0100, Hilmar Lapp wrote:
> The bioentry_relationship table is meant for exactly this purpose 
> indeed.

So, is it reasonable to use bioentry_relationship to store different
identifiers for the same bioentries, but from different or even the same
database? I'm asking that because for many genes you will find several
names/identifiers like GI numbers, gene names or locus tags and accession
numbers from different databases like KEGG, SWISSPROT, etc.

Is it possible to load such identifiers for the sequences into
bioentry_relationship without actually loading the sequence data?
How could I do so if my sequence relationships are a set of
alternative identifiers for proteins in a tab separeted file (non-redundant
sequences identifiers from PIR-NREF)?

Also, what I need is a database of sequence aliases, that would make
it easy to find identifiers for sequences in different resources (UniProt,
Kegg/COG/KOG orthologous classifications, etc.).
Do you have any suggestion on how to implement such a database using


> 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.
> 	-hilmar
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
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