This week, we've worked on finalizing our person and patient objects. After a few weeks of writing the separate parts of this program, we've finally brought them all together into a cohesive whole. The code will now read in the XML files and apply the information to each individual patient. Now that we have this functionality implemented, we should be able to begin analyzing data soon.
CREU
10/23/15
This week we split up the work among the three of us. I focused on writing a code that read in a CSV file of patient information. Later I will be using this file and file reader and applying statistical analysis on the expected versus reported ages of the patients.
10/16/2015
This week Rebecca and I worked together on creating person and patient objects in python. It had been a while since I had done this in python, so I took some time getting familiarized with how to do this. Our code is pretty basic, it takes in user input (name, smoking status, diabetes status, etc) and assigned it to a person/patient object. Next week we will be working on reworking the code so that is takes in this information from the tags in our patient files.
Rebecca’s CREU Update! 10/27/15
This week, we worked on finishing up our person and patient classes. I also created separate objects for each tag category - for example, family history and medication. At first we were reading in these tags as strings. Now we can save them as objects that contain more specific information as attributes, which will be helpful for future analysis.
Weeks 5 & 6 – Katie
I was fortunate enough to attend the Grace Hopper Celebration recently, so I was unable to make our most recent meeting. However, I did program quite a bit on the plane (I had a lot of layovers). Regular expressions are a good time.
Week 4 – Katie
Stephanie, Rebecca, and I have started discussing how we're going to integrate all of our code, since we have all begun working on parsers, Patient classes, and so on. I did some more background reading as well.
Lately we've been in a little bit of a limbo; we have a lot of the tools we'll need to begin the project in earnest, but we don't have a place to store the data, so we're at a temporary impasse with regard to that.
I also spent some time this week ensuring that the patient class is appropriately robust for the data I already have access to, and additionally tweaked my XML parser for improved flexibility.
Week 3 – Katie
This week, I read more background on the subject of not only de-identifying medical records but also on developing ways to parse the files, find medical information, and so on. It was very interesting, especially since I hadn't a lot on the subject since earlier this summer.
I also began to develop a program which will read in a patient's information from an XML file and attribute the details of their medication history, smoking status(es), etc. to a Patient object.
Week 2 – Katie
This week I started working on a Patient class, which will encompass information such as medication history, smoking status, family information, co-morbidity of disease, etc.
I have a small subset of data available to use and have been testing my parser on that. It's been fun to get back into regular expressions -- finding patterns in language, and then implementing them as robustly as possible, is something I actually really enjoy.
Week 1 – Katie
Since we're still working on finding a way to host our data in a way that enables us all to have access to it but not provide any means of accidental data leaks, I spent my week developing an XML parser. As it currently stands, the program I have written will read in an XML file with a de-identified medical record in it, find the tags within the file, and separate them.
I'm working to automate the process and make it more robust to fit the needs of the whole dataset as well.
I also re-took parts of the CITI certification course to gain more knowledge on research ethics specifically related to our project.
CREU Update! 10/16/15
Today, Stephanie and I worked on creating Person and Patient objects in Python (Katie is away at a conference, go Katie!). I've never used Python for object-oriented programming before, so I had to learn the basics of class definitions, how constructors work, etc. The objects we created are still pretty basic and static. The Person class has attributes like name and age, and the Patient class inherits these attributes along with others such as current medication. The next step will be to bring our code together with what Katie has put together, and to pull information from our XML files and link that data with each person/patient object.