I\'m working on an open source project dealing with adding metadata to folders. The provided (Python) API lets you browse and access metadata like it was just another folder. Be
To me, we can compare folder with files to HDF5 only in the relevant context of scientific data where the most important data are arrays described by a set of metadata.
In the general context, Marcus is alright when he claims that folder with files is far more portable than any HDF5. I will add that in a general context, a folder with file is far most accessible than a HDF5 file. The obvious challenge is that with "normal" folder and files, there is no need of an extra API to access data. That is simply impossible with HDF5 that keeps data and metadata in the same file.
Imagine a moment, to read your pdf file, you need a new pdf reader that understands HDF5? Imagine, to play your music, you need a music player that can decode HDF5? to run your python script, the python interpreter needs to first decode the HDF5? Or the total, to launch your python interpreter, your operating system needs to decode the HDF5? etc. I will have simply not be able to write this answer, because my OS won't have been able to launch my web browser, that won't have able to read its internal files because I previously turned everything into HDF5 (maybe a large HDF5 for everything in my hard drive).
Storing meta data in separate file has that huge advantage of working well with the huge amount of data files and softwares that already exist without any extra piece of headache.
I hope this helps.