Flexible Query Builder for DayCart and other Relational Data Sources.

Lewis Jardine, Anatoli Krassavine, Mitch Miller

NetGenics UK Ltd, 11C Park House, Milton Park, Abingdon, Oxfordshire. OX14 4RS UK.


One of the problems associated with the application of large database systems for HTS and genomics data is the problem of querying collections of databases containing complex datatypes. One recent development, the advent of object-relational technology (such as Oracle Cartridges) has simplified this problem, by allowing domain specific data to be held within standard tools rather than a mixture of relational and non-relational proprietary solutions. This at least solves the problems caused by the plethora of different databases and platforms. However, this is not enough to solve all the problems associated with data access.

Straight forward, commonly used, standard queries can be entered via forms, but exploratory, non-standard, complex queries require extensive knowledge of SQL to generate them. Since these queries typify the Discovery process either domain experts must learn SQL or they must work hand in hand with a SQL expert. Either way, this is expensive, inefficient and prone to error.

A better solution is to provide tools that domain experts can use to construct complex compound queries without the need to learn SQL. These tools must not only handle standard SQL statement but must be flexible enough to handle the domain specific data objects, such as chemical structures or genomic sequences held with for instance Oracle cartridges.

The ChemSymphony and MetaSymphony team has had considerable previous experience in the design and construction of flexible and intuitive user tools for Discovery informatics using Merlin and the Daylight toolkit. We present a flexible query builder for access to DayCart, other SQL databases and Oracle cartridges.

This tool requires absolutely no knowledge of SQL on behalf of the user enabling domain experts to construct complex queries without needing SQL knowledge.

This tool is built using component technology, which allows it to be reconfigured very easily and which also eases integration with other software. The QueryBuilder has been integrated with Spotfire to demonstrate this.

Daylight Chemical Information Systems, Inc.