I have had my RocketChat turned off for a week or so (no particular reason... just forgot to have it on!) so I missed your messages. Sorry about that!
I want to kick this project off by seeing what cTAKES can do. Can you take some encounter data that you have for a handful of patients and remove any personally-identifying information? Ideally, the data should include medical issues, drugs, codes, and important free text notes about their situation.
Once this is done, we can use this awesome tool that has cTAKES running under the hood to see the results: http://126.96.36.199:8080/index.jsp
I did some research and this is the easiest way to test out cTAKES, with the second being pulling down a Docker image (fortunately you have Linux so that will be easy as we move forward with the project).
I do realize that the US gov't has released a rather large dataset of realistic fake patient data, but I was thinking that it would be great to start with 3 or so entries from you because you have already listed a scenario in your initial email about the patient that smokes and I'm sure you have worked with patients with other unique problems. In this way, you'll know what you, the provider, expect to see from a summary perspective.
Is this okay?