[jpeloquin]

Not exactly what you asked for, but PathBank is a database that quantitatively describes a large part of what we do know: https://pathbank.org/

As far as what we don't know, I'm not sure there's a list. Lack of knowledge implies lack of awareness. I can offer one example: We don't know much about the processes by which collagen fibers are grown and assembled into μm- and mm-scale load-bearing structures in tendon, ligament, bone between embryo and adult, particularly in mammals. Or the extent to which collagen fiber structures are capable of turnover in adults; healing might only be possible by replacement with inferior tissue such as scar.

Personally, I think the complexity of biological systems, and the difficulty of observing their components directly when and where you'd want to, means that they can only be understood with the help of machines. Not necessarily using convolutional neural networks though.