BioJava provides object relational mapping
(ORM) to BioSQL 1.0 using Hibernate bindings
to objects in the
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
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:
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.
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 This is outdated, buggy, deprecated and not maintained.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.