SQL or NoSQL for structured clinical data
As usual in similar cases, I would strongly recommend that you look at Open Source solutions - well before the design phase. EVEN if you are doing something truly radical, one can always learn by standing on the shoulders of giants.

I have worked as a student on the OpenEHR project, so this interests me. It's been a while, but I would start by looking here, here and here. GIYF :-).

For a pure database recommendation, I would include the big three of Open Source databases - MySQL, PostgreSQL or Firebird. Find a system you wish to adapt. "Good programmers know what to write. Great ones know what to rewrite (and reuse)" and use the database with that - unless you have a particular requirement that precludes the chosen system's database.

There was a time I would not have recommended MySQL, but I have recently had occasion to work with it, and I was pleasantly surprised - though not having CHECK constraints is still a bit of a shock!

I note with interest in your profile that you are an experienced contributor to the stackexchange lists, so I would ask the question as to why you are choosing MongoDB? I'm not saying your choice is incorrect, I'm just wondering what it is that MongoDB has that you can't get from a "classic" RDBMS? 

My understanding is that NoSQL solutions are meant to be for coping with web-scale problems (in big data and real-time web applications), and not running simple medical centres. Even if your system was dealing with the entire population of Chile, it still wouldn't start to be "large" on the web-scale. A further point would be that I can see no valid reason whatsoever to sacrifice consistency with medical data - it might be OK for books on Amazon, but not this sort of information ("Many NoSQL stores compromise consistency" [ibid]).

In any case, I wish you well with the project.