A system is presented with a search panel for specifying search criteria for searching a database of biological information. The search panel uses the extensible markup language (XML) to send search requests to the database. A database graph generation module linked to the biological database generates a database graph representing the database schema. Once the database schema is known, another module creates joins between the database tables in order to most effectively join data from one table to another. An SQL statement incorporating the optimized joins is then used to search the biological database.