Semester Reflections

When I began working for TWC this semester, I was an Information Technology major with a concentration in Information Security.  I really thought that my interests would best fit in the Open Government Data work at the lab.  However, I fell into the Health and Life Sciences work, and it turned out to be a much better fit for me since a few weeks into this semester, I changed my concentration from Information Security to Science, Technology, and Society.  This switch stemmed from some life events that inspired me to pursue work in the ICT4D field. Now, I really just want to help people in need, and working on projects related to health is a great way to do so.

The beginning of the semester was somewhat slow.  I worked through several tutorials and read through several papers, really trying to get a feel for the work here, particularly in the health community.  I learned quite a bit about the role ontology for medical health records and about the process of mashing up data for intuitive visualization.  I was also able to provide feedback for the tutorials developed by TWC, so that they could be presented seamlessly.

About mid-way into the semester, I got involved with the SMART application project.  I was asked to take a managerial role on this project, so I set up meetings based on the schedules of team members.  I helped in the brainstorming of a project scope, and I did a great deal of background research on how to work with the SMART API.  Additionally, I learned how to code in Python and how to incorporate semantic web technologies within the code.  I was able to write a small bit of code in Python that ran on the SMART server, pulling patient medical records and printing out all of their current medical problems.  Unfortunately, this project changed direction, so I was not able to continue the work on it.  Still, it was a great opportunity to gain a broad view on Semantic technologies and their possibilities within the health field.  Each of the team members brought unique expertise to the group, and being able to listen and respond to their thoughts was very beneficial for me.

As a final push in learning this semester, I will be spending my last week here working on some simple mash-ups for the National Cancer Institute.  I am excited to be able to produce something tangible this semester and gain the skills to be effective in other roles next semester.

Continued SMART App

My past few days in the lab, I have begun preliminary coding for the SMART App. Using the SMART API, I was able to grab rdf data of patient problems from the sample patient medical data and query their names, identifiers, and resolution dates to determine each patient’s current medical problems. These problems are then displayed as a list on the SMART platform. This was all written in Python, and I think that I have reached a point where I am very comfortable programming in this language. This was also my first experience writing my own SPARQL queries, so this exposure was very helpful.

I’ve also been assigned to take the lead on scheduling meetings and addressing concerns for this project. I’ve been doing most of the background research on the Documentation for the SMART API and relaying what I learn to the group. I’ve also been organizing the necessary breakdown of the project into developing a use case, determining design and structure, and planning for a final product. I’m enjoying this part of my work here, but it can be frustrating when scheduling conflicts arise, making it difficult for everyone in the group to stay on the same page.

SMART App

This past week, I have been continuing work on the SMART App Challenge. This has involved downloading the SMART App libraries, testing sample code to pick out problems in my system, and getting acquainted with the library syntax.

During group meetings, we still have been working on the development of our project idea and solid use cases.

I’ve also been installing all of the appropriate software for this development on my laptop and have officially decided to never invest money in anything but a Mac in the future. Using my machine has presented a few setbacks, but with some extra time, I found ways to skirt around them and make everything work out.

I worked through a tutorial put together by Tim Lebo on converting CSV to RDF, and I attempted my own mash-up by throwing global female literacy data and population data into a Google Map visualization. It wasn’t the most technical implementation, but at least I got to see how the data meshed within the visualization. This was helpful in exposing me to TWC technology.

Preparing for the SMart App Challenge

I’m currently working with a group of professors and graduate students on developing an application using the semantic web and electronic health records to link data and display the resulting correlations to doctors, patients, and researchers in an intuitive way. As of now, several brainstorming meetings have been held, and project ideas have been formulated, discussed, debated, etc. While a definitive project idea has not been established, we have narrowed the scope of ideas and ruled out several that cannot be done or have already been done. Our objective is to come up with something very useful in the medical field, so it is important for us to focus on real needs. We don’t want to develop an application just for the sake of developing it.

Once we choose a project, the next challenge will be determining the extent of data that is available and how it can be used effectively. The coding will be done in PYTHON, so I am now in the process of familiarizing myself with this language.

In the meantime, I am working through the SPARQL tutorial presented at CSHALS and learning how to move data into the Triple Store on the TWC drupal site.

I am currently working on migrating external content to the TWC drupal page.

This past week, I’ve also read through a few papers related to the Translational Medicine Ontology and security factors involved in creating semantic EHRs.

Finally, by stepping through aspects of a Health Care tutorial presented at the Conference for Semantic Health and Life Sciences in Cambridge, MA, I have gained exposure with mash-ups, sparql queries, and Google visualizations.

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Preparations

In the time that I have spent working in the TWC undergraduate lab, I have inadvertently picked up aspects of Semantic Web technology. In my first few days, I helped Professor Luciano and other graduate students set up a WordPress site that would be used for an upcoming tutorial in Boston. I personally stepped through aspects of the tutorial to ensure that instructions were clear and roadblocks were not present. Since I’m on a Windows machine, some bumps were unavoidable and finally a memory leak halted further progress. This was all very helpful for those putting on the tutorial, however, since many of the attendees would be using Windows machines.

The following week I began reading up on the issues of security with healthcare data and on the technologies involved with ontology.