(May 2009 - May 2010)
Role: Master's Project
Publication: Sara Tily, Marguerite C. Murphy, Omkar Dangat, Christopher D. Smith, GO Visual Browser, Fifth International Conference on Semantic Computing (IEEE ICSC 2011), September 18-21, 2011, Stanford University, Palo Alto CA, USA.
Gene Ontology, or GO, is a large controlled vocabulary (ontology) with pre-defined relations amongst the terms defined in it. GO Visual Browser is an interactive, user-friendly application that allows surfing over controlled vocabularies. The browser interface is designed after analyzing the needs of biologists who intended to use GO, but are not able to access it due to a lack of technical knowledge about database systems. This project addresses the design, implementation and evaluation of the GO Visual Browser: a graphical interface to provide an integrated-view of Gene Ontology terms and relations. This application not only allows users to browse over Gene Ontology entries, but also provides a visualization of terms and relations associated with these terms in a particular sub-ontology. A new graphical interface was designed to simplify and unify ontology browsing. A set of "terms" is defined by each ontology. Browsing involves selecting a specific term and type of ontology relation, and then displaying an interactive map displaying all of the related terms. This application is fully functional and is platform- and browser- independent.
I was involved in the design, implementation and evaluation of a new tool for visualizing ontology terms and using groups of related terms to retrieve sequence features annotated with these terms from a genomic database. This work was recently published as a short paper at an IEEE International peer reviewed conference. Biologists commonly annotate genome and protein properties using ontology terms. While biologists have a deep understanding of the underlying biology, they rarely have a good understanding of the semantic networks used to represent domain ontologies. This paper presents the design and implementation of the GO Visual Browser: a new tool to provide visualization of Gene Ontology terms and relationships, as well as retrieval of associated genomic data. Browsing involves selecting a term and type of ontology relationship, and then displaying an interactive map with all of the related terms. This map can then be used to search a genome database for all features, related sequences, and metadata annotated with the selected ontology terms.
This tool code is fully functional and is being distributed as open source software. It is implemented in AJAX environment for active communication between client and server. The system is designed as an accessible Web application using PHP5 running on a Unix-based server. This application has three-tier Web architecture. It uses XML files to generate graph containing search results. This application is compatible with all major browsers.