Monthly Archives: February 2016

Although the code I wrote over the last few weeks was primarily in script format, I put some time in over the weekend to create Python classes in order to analyze medication history more effectively. Building off of my previous Medication class, I introduced a time attribute, so that I can keep track of when the medication was being taken (before/during/after DCT).

During week 15, I worked on extracting diabetes mentions from each medical record and writing them to a CSV file. I formatted the file based on what will work best for Stephanie when she goes on to analyze the CSV in R. It took me a while to work out all the bugs, but I had an accurate CSV by the end of the week. Just skimming the file I could see that a surprising number of records never mention the fact that the patient has diabetes.

Now that I've developed the script to go through each record, extract diabetes mentions, and write them to a CSV, doing the same with other tags will be much easier. I also created a CSV file detailing the patient's smoking status. Though this file was relatively simple for me to create, it will be harder to analyze since someone's smoking status can change over time.

Currently, I'm working on going through this same process to create CSV files for family history and other tags.

Last week, Simmons closed the school due to snow on Monday, so we didn't meet; instead, I worked on extracting medication data from tags. I've been using linked lists to keep track of which medications are mentioned when.

This week, I ran into a couple of issues with my code, but I've been working to resolve them, and have also been reading more about methods for addressing temporal issues in code. More updates to follow!

This week I will begin to work on the problem of finding discrepancies of smoking statuses. In our weekly meeting we discussed some of the challenges that will come with this - primarily that smoking status can change in a much more complicated way than diabetes status. In the case of diabetes the patient must have had diabetes, so if they did not we knew there was a discrepancy. Smoking status, on the other hand, can switch back and forth many times However, if a patient is listed as a smoker in the first visit, and then as never having smoked in any later visits then there is a discrepancy. This is definitely going to be an interesting project.

This week, we worked on completing our poster proposal. I did a lot of background reading for this, mostly from the Journal of Biomedical Informatics. They recently released a special volume full of articles pertaining to the i2b2 Shared Task, which is where our corpus of records came from. Seeing how other teams approached the task was interesting, as well as seeing if they addressed missing and inaccurate data.

This week we collaborated to finish a poster presentation for the 2016 Tapia conference. We also read journal articles from the journal of biomedical informatics. The articles were pertaining to the 2014 i2b2/UTHealth NLP shared task, which is where we are getting the information for our research.