User Interface for Chado Database Schema


Kalpesh Gada

Oral Defence Date: 

Wednesday, December 3, 2008 - 16:30


SCI 241


4:30 PM


Professors Murphy, Petkovic & C. Smith (Biology)


The use of relational databases in the field of science and technology has increased tremendously over the past few years. This has motivated biologists (and other scientists) to make use of databases for storing and retrieving data. The data stored includes information about particular biological species and/or collections of closely related species. One such database schema based on relational database technology is “Chado”, which is under development by GMOD (Generic Model Organism Database) and is freely distributed for use by anyone. The Chado schema is a relational, highly extensible and sophisticated schema consisting of approximately 133 tables. To provide a better understanding of this complex schema for the user, the tables have been grouped into distinct modules, with strictly defined dependencies/relationships. However, many users of this schema are not tech savvy, and frequently it is difficult and time consuming for them to explore and use this schema for their research and experiments. To promote easier use of the Chado schema, the project presented in this report describes the design, development and verification of an easy-to-use Graphical User Interface that allows interactive exploration of the Chado schema. This interface represents the schema as a graph where tables are represented as nodes and relationships between the tables as edges between the nodes. The user can zoom-out to see all of the nodes/tables and their edges/relationship at one glance, or zoom-in to view more details about a specific table or group of tables and their relationships with other tables. The user can right click on any table/node to view all of its attributes, and then select any attribute for output and/or to specify selection criteria. This information is used to form a simple SQL query to retrieve the collection of data identified by the user. Our prototype is fully functional, and satisfies all of the functional requirements we identified.

Kalpesh Gada

Chado User Interface, Chado Schema GUI, Chado UI, Chado Interactive User Interface