Persistent BioPerl

Abstract

I present BioSQL, a generic and highly extensible relational model for storing biological sequences, sequence clusters, genes, sequence features, sequence and feature annotation, and ontology terms. BioSQL also represents the interoperable persistence API among the Bio* life science programming toolkits (BioPerl, Biojava, Biopython, BioRuby), each of which has a language-binding to the BioSQL schema. I specifically present the Bioperl-db software, which in a transparent manner makes BioPerl objects persistent using BioSQL.