An Informatics Based Tumor Specific Data (TSD) Model with Pathology Annotations To Support Translational Research in Inter and Intra- Institutional Tumor Repositories
Harpreet Singh, Waqas Amin, Anil V Parwani. University of Pittsburgh, Pittsburgh, PA
Background: The databases model is designed to facilitate complex clinical and research functions and incorporate 'real-time' updating of information. This technically complex process required identifying the precise role of the Honest Broker and research user's interaction with data in the relational database. Our aim was to provide a simple user interface with powerful query capabilities to access de identified pathology and outcome data.
Design: The database model provides a web-based data annotation and query engine supported in a three-tiered architecture, implemented on an Oracle Application Server v10.1.2.3 running on a Windows 2007 and Oracle RDBMS v.11.1.0 running on a Community Enterprise Operating Systems (Centos 5.3.) virtual host definitions which is supported by IBM Cluster hardware. This model utilizes the Oracle http server and mod_plsql extensions to generate dynamic web pages. This application is flexible to facilitates investigators to search on de-identified information.
Results: This informatics supported TSD model has been in use for a decade to support translational research at local and cross institutions. An overview of the legacy database is provided briefly in the following table. This database model integrates a spectrum of data sets including clinical pathology, follow-up, molecular and imaging in relational database that allows the user to query across all types of datasets. The access to database can be regulated as per user authentication.
|Data Bio-repository and Project Name||Multi-institute(M) / Single Institute(S)||Total patients||Data Access :||Data Access:||Data Source|
|Public or Statistical Query||User Interface (clinical and Research)||Data Annotation, Electronic data import/export|
|Pennsylvania Cancer Alliance Bioinformatics Consortium (Prostate, Melanoma, Breast)||M||∼3000||Yes||Yes||Both|
|Early Detection Research Network (Colorectal and Pancreatic Virtual Biorepository)||S||2614||No||Yes||Both|
|SPORE (Head and Neck Neoplasm Virtual Biorepository)||S||7752||No||Yes||Both|
|Cooperative Prostate Cancer Tissue Resource||M||6063||No||Yes||Both|
|Gynecologic Cancer Research Center of Excellence||M||Under enrollment||Yes||Yes||Both|