BioPerl db
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bioperl-db and BioSQL
The bioperl-db package is intended to enable the easy access and manipulation of sequences in a relational databases via a Perl interface. Currently the bioperl-db interface is implemented to support databases in the Mysql, Postgres and Oracle formats.
The database schema itself is not specified in the bioperl-db package but in the BioSQL project. It is worth mentioning that most of the familiar Bioperl objects map directly to tables in the Biosql schema. Therefore object data such as sequences, their features, and annotations can be easily loaded into the databases, as in:
$seqobj->store();
History of BioPerl DB
- Ewan Birney's SRS replacement.
- BioSQL project and schema. See also usage examples.
Current status
Hilmar Lapp is the current project lead on this project. It is still somewhat of a collaboration with our BioJava, BioRuby, and Biopython brethren.
An official release is expected by early 2006 soon. A publication is also in preparation.
The latest code
The latest, and not completely tested, code can be viewed here:
You can download it by following the instructions in Using Git. The repository name is bioperl-db.
Documentation
- Hilmar's 30 slide BOSC 2003 presentation on Persistent Bioperl.
