Difference between HDF5 file and PyTables file
PyTables files are HDF5 files.
However, as I understand it, PyTables adds some extra metadata to the attributes of each entry in the HDF file.
If you're looking for a more "vanilla" hdf5 solution for python/numpy, have a look a h5py.
It's less database-like (i.e. less "table-like") than PyTables, and doesn't have as many nifty querying features, but it's much more straight-forward, in my opinion. If you're going to be accessing an hdf5 file from multiple different languages, h5py is probably a better route to take.