Coincidentally, we’ve also been working on data in BIDS formatted directories, and have just opened the first registration PR for BIDSTools.jl which is like a lightweight version of pybids: it parses metadata from a BIDS directory into an in-memory format which is simple to query.
Because the BIDS conventions are rather useful for data layout of medical imagery (regardless of whether it’s neuro related), we’ve been quite flexible and unopinionated about metadata schema so far, though that could be layered on top. I’d also note that we’re working with relatively small datasets (mostly neuro and breast MR imaging + spectroscopy) so we haven’t worried much about performance yet (eg caching of metadata indices).