[Bioperl-l] Newbie Questions: bioperl, bioperl-db, and GO

Hilmar Lapp hlapp at gmx.net
Thu Apr 14 03:00:09 EDT 2005

On Wednesday, April 13, 2005, at 11:44  PM, Jamie Sherman wrote:

> The second part of the question is more about after I can collect all 
> the information into the program and associate it with the protein 
> expression data what is the best way to manage that information to 
> take advantage of clustering abilities of bioperl.

I can't comment on that part as I don't know about those modules.

>  Should I load them into BioSQL and if so where do I look for 
> documentation to learn the interface to BioSQL. I noticed a lot of the 
> perldoc pages in the Bio::DB:*** seemed to be fairly sparse.

The vanilla version of biosql doesn't store expression data.

(Some of) the Bio::DB::BioSQL PODs (e.g., BasePersistentAdaptor) you 
will want to read if you want to become more sophisticated on how to 
query the database using the bioperl object model instead of SQL. If 
you want to understand more of the schema then you should check out 
what's in the doc directory in the biosql-schema repository, 
specifically the ERD and the schema-overview.txt document.


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

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