I would store the original data unaltered as files.

Then I would index and transform it into the lowest common denominator formats, probably something like this:

For text, plaintext with header-like fields. For images and video, the most commonly readable formats.

Then I would build index database(s) on top, probably SQLite.

And on top of that, I would make a lightweight web-based system for querying and categorizing.

This way, the data modification happens only one way, and it is easy to maintain transparency and clarity of process. You never lose your original data, so if there’s a problem, you can go back one step before the problem. And no relying on proprietary or low-support data formats.