Emily Doughty, Bioinformatics and Computational Biology
Improvement on Automatic Method for Mutation Extraction and Disease-Relationship Annotation for Mutations for the Biomedical Community
Faculty Mentor: Dr. Maricel Kann
Associating mutations with disease phenotypes is fundamental for developing novel tools for diagnosis and prognosis of cancer. Most of the mutation-phenotype relationships are buried in large biomedical literature databases such as PubMed. This research has two focuses. One is to improve the specificity of the automatic text-mining method Extractor of MUtations (EMU) which was created in Dr. Maricel Kann’s lab to find disease-associated mutations. The second part is to use EMU for a semi-automatic evaluation of five diseases and categorize mutations that are not yet in the manual databases OMIM and SWISS-PROT. I will be working to increase EMU’s precision of finding the correct gene per mutation (currently .75 precision) by associating genes to mutations based on proximity. For the second part of this work, I will be manually curating five diseases for mutational information and disease-association. The information gained from curation will be used to evaluate EMU’s gene finding methods and will be made available online for visualization for use for the biomedical community.
When and how did you find out about the URA program?
I found out about the URA program through my mentor about six months prior to the deadline. She mentioned it as a future possibility for fall research work especially since I had just completed a project in my lab.
Was the application difficult to complete? How much did your mentor help you with the application?
The application was very easy, you just need to make sure you have a clear focus, a definite goal and plan to achieve that goal. Basically, you just have to clearly state what you want to do, how you want to accomplish it, and so forth. It's especially important to have thought out your project thoroughly beforehand so your application is not vague and contains no ambiguity. My mentor reviewed my application when I completed it and offered any suggestions as needed. The whole process only took me a few days to complete.
How much time do you put into it?
I worked on the application over the course of a few days. I knew what I wanted to do, made a short list of points to include, and wrote the proposal. I found the process straightforward, quick, and simple.
What have you gained from being a URA scholar?
From working on my URA, I've gained research experience relating to the process of writing proposals, following that proposal, and staying on a deadline. I've also gained a multitude of information during the monthly URA meetings.
What is your most interesting research activity?
My most interesting research activity has been being first author on a paper that was just accepted into the journal Bioinformatics. On that project, we developed an automatic method that extracts disease-related mutations from the biomedical literature. I've been working on that project since June 2009 and to see it finally out there in the community is a major relief.
How did you know this was the project you wanted to do?
The work I'm doing is a problem that has bothered me since I started working on the EMU project in my lab. Being able to address it in some way has been a goal of mine for some time.
What academic background did you have before you started?
I am a bioinformatics major with minors in both computer science and statistics. I've worked in Dr. Maricel Kann's bioinformatics lab since June 2009. My URA work is my own continuation of a project I've been working on in my lab and was just published in Bioinformatics.
What has been the hardest part about your research? The most unexpected thing?
The hardest part (but should have been expected) was that when you get more into your work, your focus will shift slightly. It is very hard sticking exactly to the proposal you write since science (at least for my work, and I assume it is similar in other disciplines) can be unpredictable. Time lines change, you encounter lengthy problems and so forth. You should expect these problems to arise but this does not fully prepare you for when it does.
What is your advice to other students about getting involved in research?
Talk to students in research, ask your advisor about possible research opportunities in your department, and get in contact with the appropriate people. Also, make sure you have the time and commitment for a project - you can't start in September for example and then decide to stop coming in to the lab (or where ever your work is set up) and not contact any one.
What are your career goals?
I plan to continue on to graduate school towards a doctorate in bioinformatics. I'm not sure at this time what my specific focus will be. From there, I can continue in a research environment or be a resident bioinformatician for a lab.