[BioSQL-l] Gene Cluster

[Raoul Jean Pierre Bonnal]

Dear Hilmar,

Il giorno ven, 18/01/2008 alle 20.59 -0500, Hilmar Lapp ha scritto:
> Hi Raoul,
> 
> I have done this in the past using the bioentry_relationship table.  
> This assumes that the "genes" (or, more generally, the members of the  
> cluster) are bioentries, not seqfeatures. If you use BioPerl to read/ 
> process/represent the clusters, and your are using the Bio::ClusterI  
> interface for that (any of the Bio::Cluster::* modules, for example),  
> the Bioperl-db should support mapping those to the schema.
Using bioentries is right if you have an entry which represents a single
cluser. Unfortunately I have to represent clusters inside "complete"
genome, so a bioentry can have multiple clusters. 

> Obviously, you can do the same for seqfeatures using  
> feature_relationship.
Watching at BioSQL' schema, this seems to be te only solution for
representing clusters in a general way.
Now which is for you the most correct Feature Key misc_feature or
source ?

I'm using BioRuby and working on it for interfacing it with BioSQL

Skype: ilpuccio

--
Ra