Visualizing and Querying General Application Schema


Ashish Kshirsagar

Oral Defence Date: 



SCI 241


Professor Murphy, Professor Petkovic,and Assistant Prof. Chris Smith (Biology)


Biologists and other researchers need tools to extract information from large and complex biological databases. First, the biological databases contain complex data types varying from species to species and contain a lot of tables with many relationships. Second, the researchers and biologists are not familiar with querying the database for information. These two factors have engendered a need for simple user friendly query generating tools. User Interface for Chado Schema is a query generating tool developed at SFSU used locally for exploring and understanding the Chado schema [5], a relational schema developed by GMOD group [25] to manage genomic data for organisms like Arabidopsis, zebrafish, and mouse. This tool displays the tables of a relational database as nodes in a graph, and the primary key-foreign key associations between tables as edges. Query specifications are entered graphically by right clicking on nodes to choose attributes for output or to specify selection criteria. In addition to this graph, there is a control panel providing various features for interaction with the graph. Interaction allows biologists to better understand the database schema and to extract appropriate input and output attributes needed to form simple select-project-join SQL queries. Since the main motive of this tool was to visualize the Chado schema, it was designed in such a way that it only processed Chado schema data. The primary goal of the new work presented in this paper is to allow this tool to work correctly with any well-formed relational schema. This goal was realized by developing an SQL parser to processes the SQL DDL Statements used to create the schema and to pre-configure the graph display software. This software is deployed as a Java Web Start application that executes remotely via a standard web browser. This software was tested and validated by manually verifying that it correctly displays graphic output for two complex schemas.


Relational Schema Visualization, Relational Schema Parser, Java Web Start Application, Chado Schema, Chado Schema User Interface, GMOD


Ashish Kshirsagar