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Symposium - New Frontiers in Digital Pathology
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A decade of experience in the development and implementation of tissue banking informatics tools for intra and inter-institutional translational research
Waqas Amin, Harpreet Singh, Andre K Pople, Sharon Winters, Rajiv Dhir, Anil V Parwani, Michael J Becich
J Pathol Inform
2010, 1:12 (10 August 2010)
Tissue banking informatics deals with standardized annotation, collection and storage of biospecimens that can further be shared by researchers. Over the last decade, the Department of Biomedical Informatics (DBMI) at the University of Pittsburgh has developed various tissue banking informatics tools to expedite translational medicine research. In this review, we describe the technical approach and capabilities of these models.
Clinical annotation of biospecimens requires data retrieval from various clinical information systems and the de-identification of the data by an honest broker. Based upon these requirements, DBMI, with its collaborators, has developed both Oracle-based organ-specific data marts and a more generic, model-driven architecture for biorepositories. The organ-specific models are developed utilizing Oracle 22.214.171.124 server tools and software applications and the model-driven architecture is implemented in a J2EE framework.
The organ-specific biorepositories implemented by DBMI include the Cooperative Prostate Cancer Tissue Resource (
), Pennsylvania Cancer Alliance Bioinformatics Consortium (
), EDRN Colorectal and Pancreatic Neoplasm Database (
) and Specialized Programs of Research Excellence (SPORE) Head and Neck Neoplasm Database (
). The model-based architecture is represented by the National Mesothelioma Virtual Bank (
). These biorepositories provide thousands of well annotated biospecimens for the researchers that are searchable through query interfaces available via the Internet.
These systems, developed and supported by our institute, serve to form a common platform for cancer research to accelerate progress in clinical and translational research. In addition, they provide a tangible infrastructure and resource for exposing research resources and biospecimen services in collaboration with the clinical anatomic pathology laboratory information system (APLIS) and the cancer registry information systems.
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