Thank you everyone for your replies.
@byrn
I am sorry, but there are a lot of links on the website you indicate.
Which one is it? The linux files are specific for certain distributions which is suspicious as I would expect hdf.jar + native libraries which are not compiled for different distributions. The file for Windows contains an MSI installer.
@kittisopikulm
Using the JNI library from Zurich University seems to be the better approach. The lack of documentation is a problem, though.
@gheber
The query language approach might be helpful, but we are not looking for that at the moment.