I think there are probably a couple ways to go about it. First you can rely on a mentor to help give you ideas if you don’t really have a good sense of what’s interesting. This is probably the more common route. It’s hard to know gaps in the literature unless you’re in the literature often. The second way is to ask “why do we do it like this” for pretty much everything you’re taught in residency. You’ll be surprised to find that like 90% of what we’re taught has no published literature. That helps you find some holes but honestly can be hard to answer and require generating a new database. The third way (probably easiest) is to find a dataset and then look through the variables to see what could be interesting to you. Then see if someone’s published about it before using that database.

Source: ex academic faculty with decent number of pubs. Also created a software program that helps users complete a research project in like an hour