The entry point for bio4j documentation is at the main bio4j repository; if you don’t know exactly what you are looking for, go there:

In general, bio4j documentation is written in markdown, and it is kept together with the corresponding sources, inside the repository docs folder. This way docs are automatically in-sync with versions, and we can easily maintain documentation for different versions.

If you feel that something is incomplete, can be improved or is just wrong, just open a pull request!