Biomedical informatics: development of a comprehensive data warehouse for clinical and genomic breast cancer research

Author:

Hu Hai1,Brzeski Henry2,Hutchins Joe3,Ramaraj Mohan3,Qu Long4,Xiong Richard4,Kalathil Surendran3,Kato Rand3,Tenkillaya Santhosh3,Carney Jerry3,Redd Rosann5,Arkalgudvenkata Sheshkumar4,Shahzad Kashif4,Scott Richard4,Cheng Hui4,Meadow Stephen3,McMichael John4,Sheu Shwu-Lin3,Rosendale David6,Kvecher Leonid6,Ahern Stephen6,Yang Song2,Zhang Yonghong2,Jordan Rick2,Somiari Stella B2,Hooke Jeffrey7,Shriver Craig D7,Somiari Richard I8,Liebman Michael N8

Affiliation:

1. Windber Research Institute, 600 Somerset Avenue, Windber, PA 15963, USA. h.hu@wriwindber.org

2. Windber Research Institute, 600 Somerset Avenue, Windber, PA 15963, USA

3. Teradata, Division of NCR, Dayton, OH, USA

4. Management Science Associates, Rockpointe, PA, USA

5. Teradata, Teradata, a Division of NCR, Dayton, OH, USA

6. Windber Professional Services, Windber, PA, USA

7. Walter Reed Army Medical Center, Washington DC, USA

8. Windber Research Institute, 600 Somerset Ave., Windber, PA 15963, USA

Abstract

The Windber Research Institute is an integrated high-throughput research center employing clinical, genomic and proteomic platforms to produce terabyte levels of data. We use biomedical informatics technologies to integrate all of these operations. This report includes information on a multi-year, multi-phase hybrid data warehouse project currently under development in the Institute. The purpose of the warehouse is to host the terabyte-level of internal experimentally generated data as well as data from public sources. We have previously reported on the phase I development, which integrated limited internal data sources and selected public databases. Currently, we are completing phase II development, which integrates our internal automated data sources and develops visualization tools to query across these data types. This paper summarizes our clinical and experimental operations, the data warehouse development, and the challenges we have faced. In phase III we plan to federate additional manual internal and public data sources and then to develop and adapt more data analysis and mining tools. We expect that the final implementation of the data warehouse will greatly facilitate biomedical informatics research.

Publisher

Future Medicine Ltd

Subject

Pharmacology,Genetics,Molecular Medicine

Reference16 articles.

1. Hu H, Brzeski H, Hutchins J etal: Bridging genomic and clinical data: introduction to a teradata warehouse for high throughput research. Proceedings of the 8th World Multi-Conference on Systemics, Cybernetics, and Informatics VII, 52-56 (2004).

2. Inmon WH, Kelley C: Developing the Data Warehouse. QED Publishing Group (1993).

3. Kimball R: The Data Warehouse Toolkit: Practical Techniques for Building Dimensional Data Warehouses. John Wiley & Sons, Inc., NY (1996).

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