Barrett Honors College Thesis

Back when I was getting my undergraduate degree at Arizona State, I was responsible for writing a Thesis my senior year to satisfy the requirements of graduating from the Barrett College. I recently dug it out of an old file and though it'd be fun to post it...

Titled NetSynthesis: User-Initiated Synthesis of Biological Networks, the project was (to modern standards) a basic AJAX application that allows users to map protein and genes based off a given query. After making a search, the system would return a "Did you mean..." type of result. After the user selected the keywords to actually search for, a full search would be conducted.

Here's the abstract. The full paper can be downloaded here.

NetSynthesis is a prototype that allows users to synthesize their own gene-drug, gene-disease and protein-protein interaction networks through queries to a specialized database of Medline abstracts. While NetSynthesis delivers high quality results, users have to wait for a substantial amount of time for all results to be displayed. A new interface is created that utilizes PHP, Java, HTML, JavaScript, MySQL, and AJAX technology to deliver a highly dynamic and robust user experience. Users can now receive partial results when the NetSynthesis process modules retrieve and extract all relevant results.

The NetSynthesis prototype includes a Query Expander, which is designed to provide a list of related terms for the keywords specified in a query. User a combination of synonyms, terms found in definitions of MeSH terms, ancestors and descendents, NetSynthesis provides a substantial list of alternative keywords for a user to choose from before submitting the query to the processing modules. Once the user selects which keyword to include in the final query, results are then displayed to the user. In this fashion, results may be viewed by the user as the system continues to look for more results. This new interface can benefit biomedical researchers in conducting their research.