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

Richard Holland holland at ebi.ac.uk
Thu Jun 7 07:33:25 UTC 2007

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Sounds great.

BioJava users shouldn't need to change anything to get this to work as
PostgreSQL JDBC connection objects already require you to specify a schema.


Hilmar Lapp wrote:
> 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 option.
> 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
> --===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
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