"TMAtrix"– A WEB-BASED RELATIONAL DATABASE FOR COMPLETE TISSUE MICROARRAY DATA ADMINISTRATION

http://www.genetics.ucla.edu/tissuearray/public/tmatrix.html

David B. Seligson, MD
Assistant Professor
Director, UCLA Tissue Array Core Facility
Department of Pathology and Laboratory Medicine,
UCLA
Los Angeles, CA USA

David B. Seligson, MD 1
Stefan Deusch, PhD 2
Khy Huang 2
Sheila Tze, BS 1
Robert Dennis, PhD 3
1 UCLA Tissue Array Core Facility, Department of Pathology and Laboratory Medicine, David Geffen
    School of Medicine, UCLA
2 Interactive Media Group, Department of Medical and Molecular Pharmacology, David Geffen School of
    Medicine, UCLA
3 Interactive Media Group, Department of Biological Chemistry, David Geffen School of Medicine, UCLA

Background: Tissue microarray-based studies involve the collection and utilization of abundant tissue resources, the administration of voluminous and varied data sources and the interaction of several layers of personnel. This presents a critical bioinformatics challenge led by the need to manage and manipulate ever increasing data pools, and to do it in an intelligent and streamlined fashion. Only a database system able to collect, contain and present multiple datasets of TMA information will take us from limited ‘snapshot’ investigations, to a better understanding of the fluid and interactive nature of gene marker expression relative to disease. Further maturation, standardization and growth of the platform relies on the development of foundational data management tools.

Design: The UCLA “TMAtrix” tissue microarray relational data model linking over 700 data fields was developed on a Linux development database server (Helsinki, Finland), a stable version later transferred to a SUN 6500 Enterprise server (Palo Alto, California) hosted and maintained by the UCLA Advanced Research Computing Cooperative (ARCC). Using an open source application framework, Expresso (Jcorporate; Freeport, Bahamas; http://www.jcorporate.com), user interfaces and server-side classes were developed to manage, query, and maintain all TMA data. This data management system runs on an Apache Tomcat Server, that consist of a Web server and the Catalina servelet engine. Data is managed in an Oracle 8i Relational Database Management System (RDBMS). The system is interfaced with a ScanScope high-resolution whole slide image-scanning workstation, (Aperio Technologies, Inc., Vista, California), from which images are captured and served upon query from the database application.

Results: The Web-based system described handles all of the operating functionality required to manage tissue microarray studies, and provides a foundation for interaction, growth and data standardization. It has removed our previous need for disparate and difficult to oversee data files, increasing efficiency, reducing error, and allowing multiple users data access.

Conclusion: The growth and utility of tissue microarray research platform presents a concomitant challenge in the integration and organization of the resultant supporting data files. We present here an open-source Web-based relational database solution in response to that need, in recognition of both current, and potential future, functionalities.