[Bioperl-l] PostgreSQL schema support in BioSQL and bioperl-db

Hilmar Lapp hlapp at gmx.net
Thu Jun 7 00:45:14 UTC 2007

I have added support to BioSQL and bioperl-db for schemas in  
PostgreSQL. A schema in PostgreSQL is more or less a namespace for  
database objects (tables, indexes, views, etc) within a database.

(A database in PostgreSQL is similar to the concept of a user in  
Oracle or MySQL, and therefore for the latter two schemas are  
synonymous with a user. [Not sure I'm still up-to-date on this for  
MySQL, but at least that's what I recall.])

When using the load_{seqdatabase,ontology,ncbi_taxonomy}.pl scripts,  
you specify the schema in which BioSQL resides using the --schema  

If you are using bioperl-db as a library, the Bio::DB::BioDB->new()  
call also accepts a -schema named parameter, and Bio::DB::DBContextI  
objects have a $dbc->schema() property for getting/setting the  
schema, Bio::DB::SimpleDBContext->new() accepts a -schema parameter,  
and you may also add the property to the .bioperldb connection  
parameter file (-schema => 'yourschemahere').

Thanks for Brian Osborne for being the instigator (and tester, and  
for adding the code to load_ncbi_taxonomy.pl - I came too late).

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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