BioUML workbench API documentation (v. 0.7.5) available in two forms:

• generated by javadoc
• generated by Together Control Center (http://www.togethersoft.com).
  This version of documentation includes UML class diagrams for all packages.

You also can download both versions of documentation as zip files.

• javadoc.zip (4.3 mb)
• javadoc_together.zip (6.4 mb)
  

If you already have downloaded BDK (BioUML development kit), you can use ant javadoc task to generate the documentation:

ant javadoc