Tuesday, May 29, 2007

About the Cohort Definition Tool

As promised, some details about the project...

My original application was for the Clinical Data Visualization Tool, but a slight re-allocation happened and I'll be working with the Cohort Definition Tool.

First of all, the defining the term Cohort is important. At least for me it was, since I wasn't familiar with it. According to the trustful Wikipedia:

"In statistics and demography, a cohort is a group of subjects — most often humans from a given population — defined by experiencing an event (typically birth) in a particular time span. (...)"

Even though this is a very general definition, it's quite applicable to this context. Medically speaking, and particularly in OpenMRS, a cohort is a set of patients with common characteristics. These can be very diverse, from gender, age, types of drugs taken, etc... After defining a cohort, one should be able to act on that set of patients as appropriate, e.g. scheduling an encounter for all male subjects with CD4 count<350.

Darius, who will be mentoring me for the Summer has made very significant progress with the Cohort Builder, as seen on OpenMRS demo website:
A user can already search cohorts according to many variables, conveniently organized in categories and available through the tabbed interface. Cohorts can also be combined with AND and OR operators, or by defining a more complex expressions. The searches can be saved for later use and are stored with cached results (which may not be always accurate, but guarantee a fast UI response to user queries and a good estimate of the number of patients).

As complete as the described tool may be, there's always room for improvement, as with any piece of software. Currently the patients' names are listed together with their age and sex. My work will focus on graphical cohort visualization alternatives. One of the main goals is to have this data organized in one or several plots, customizable by the user. The exact way in which this will be done is still to be decided, but the adopted solution should provide a clean, fast and useful way of viewing cohort data.

More on this to come...


Friday, May 25, 2007

Hi everyone!

Summer of Code 2007 is on! I will be using this space to post the ups and downs of this beachless Summer.

"OpenMRS formed in 2004 as a open source medical record system framework for developing countries — a tide which rises all ships. OpenMRS is a multi-institution, nonprofit collaborative led by Regenstrief Institute, Inc. , a world-renowned leader in medical informatics research, and Partners In Health, a Boston-based philanthropic organization with a focus on improving the lives of underprivileged people worldwide through health care service and advocacy."

I heard about OpenMRS a few months ago, and got interested from the moment I checked out the nature of their work. It's a great thing to be able to use what I've learned to help those who need the most, and that's the main reason why I chose to get involved in an OpenMRS project.

Just a little something about myself... This is not my first SoC, I also participated last year, implementing some SVG filters support for Inkscape.org, which was a really great project to work on. SoC is an amazing initiative, especially for those not-so-familiar with Open Source development (as I was, until last year) for so many reasons... I especially enjoyed the amazing personal experience I got out of it, the community bonding that is created among the participants, all the new things you learn about the mentoring organization and the fact that I helped to build something that will be put in use by so many people (check out the Gaussian Blur applications on Inkscape 0.45).

For all this year's OpenMRS SoCcers (students, interns or whatever you'd like to call them:)), good luck for your projects, I'm sure you'll have a great time!

This introductory post explains the WHY, stay tuned for the WHAT and HOW of my project ;)