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Undergraduate Researchers

Laura Anzaldi, SURF Scholar

Developing Root-Based Semantic Vocabulary

Information related to medicine, biology and chemistry is stored by a number of different sources, each of which uses a different vocabulary. This makes combining or sharing information very difficult, as for literal, pattern-matching computers, different vocabularies are completely different languages. Therefore it is necessary to develop a root-based vocabulary (mirroring Latin) to act as a standard. This is advantageous, as once a common set of roots has been established, the meanings of compound words become intuitive. Adding vocabulary, which is essential for the exponentially growing field of biology, could not be easier. New vocabulary can be formed by combining different root words, or if need be, creating new ones.

In order to form this new vocabulary, specialists in biology selected a diverse, extensive and representative collection of ontologies. I parsed these ontologies and entered them into database tables, in order to facilitate extracting and querying information. By using parent-child relationships between the terms, I wrote a program to recreate trees showing the hierarchical nature of words in the ontologies.

The final stage of my project was to create a user interface, a website, so that biologists and chemists would be able to easily query the database to collect information. These experts will be able to do what computers cannot…judge how suited a word is to serve as a root. Proper root words are easily concatenated, easy to say, and usable in a wide variety of contexts. A standard root-based vocabulary will streamline communication and encourage unity in information between different scientific companies and organizations

How did you find out about SURF (Summer Undergraduate Research Fellowship)?

I saw a flier in the Honors College lounge and thought it sounded like a wonderful opportunity.

How did you know this was the laboratory you wanted to work in?

I worked in the Chemical Sciences lab this summer, which I applied for because I was interested in gaining some experience with lab work. However, I was placed in a bioinformatics position, which gave me the unique opportunity to use computer science to solve problems in biology.

   

Is this your first independent research project?

Yes, before this I had never done research.

How much time do you put into it?

SURF is full time for 11 weeks.

What academic background did you have before you started?

I had just completed my freshman year of college at UMBC, so nothing more than introductory computer science classes.

Was the application difficult to do?

No, and I really liked how you applied for a lab rather than for a specific project.

What is your advice to other students about getting involved in research? 

Be open minded in selecting where/to what projects you apply.  You might be surprised at what you stumble across.

What has been the hardest part about your research?

I dealt with a lot of technical difficulties and struggled a bit with overall inexperience.

 

What was the most unexpected thing?

I was surprised how long the project took me. When I heard an initial description at the beginning of the summer, I did not expect it to take 40 hours a week for the full 11 weeks!

 

How does your research relate to your work in other classes?

My research used all of the introductory level computer science concepts, and I think I will find it relates even more as I continue into more upper level classes. I had to teach myself about databases, Perl, and a little web development