You can uninstall or removes an installed libbiojava-java package itself from Ubuntu 12.04 LTS (Precise Pangolin) through the terminal,
$ sudo apt-get remove libbiojava-java
If you would like to remove libbiojava-java and it's dependent packages which are no longer needed from Ubuntu,
$ sudo apt-get remove --auto-remove libbiojava-java
If you use with purge options to libbiojava-java package all the configuration and dependent packages will be removed.
$ sudo apt-get purge libbiojava-java
If you use purge options along with auto remove, will be removed everything regarding the package, It's really useful when you want to reinstall again.
$ sudo apt-get purge --auto-remove libbiojava-java