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BioJava BioSQL ORM

BioJava provides object relational mapping (ORM) to BioSQL 1.0 using Hibernate bindings to objects in the org.biojavax packages.

BioJavaX Design

BioJavaX was officially released with BioJava1.5. It extends the org.biojava API’s and was designed to very closely match the BioSQL schema. This made ORM of BioJava to BioSQL much more straight forward and brought the BioJava object model much closer to that used by BioPerl.

Hibernate Mapping

Hibernate is currently used as the ORM provider for BioJava. Mapping is defined using xml config files. These files formally define where objects are written in the database.

Hibernate mappings are currently defined for the following RDBMS’s:

JPA and Annotations

In the near future it would be desirable to update BioJava to make use of JPA and Annotations to define entity mappings. This would offer several advantages.

  1. It would be possible to define a JPA entity manager which would not need to know which ORM system is being used. Currently we are limited to Hibernate.
  2. Annotations could be used in classes that form entities removing the need for XML configuration.
  3. If XML configuration is prefered then there would not be a need for one per RDBMS.

Legacy Mapping

BioJava does contain a legacy mapping to the Singapore release of the BioSQL Schema. This is outdated, buggy, deprecated and not maintained. We retain it only for backwards compatability and reserve the right to drop this support at any time in the future. The mapping is not compatable with any other Bio* project. We strongly advise against using it.