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

Hai Hu; Henry Brzeski; Joe Hutchins; Mohan Ramaraj; Long Qu; Richard Xiong; Surendran Kalathil; Rand Kato; Santhosh Tenkillaya; Jerry Carney; Rosann Redd; Sheshkumar Arkalgudvenkata; Kashif Shahzad; Richard Scott; Hui Cheng; Stephen Meadow; John McMichael; Shwu Lin Sheu; David Rosendale; Leonid Kvecher; Stephen Ahern; Song Yang; Yonghong Zhang; Rick Jordan; Stella B. Somiari; Jeffrey Hooke; Craig D. Shriver; Richard I. Somiari; Micheal N. Liebman

doi:10.1517/14622416.5.7.933

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

Hai Hu^*, Henry Brzeski, Joe Hutchins, Mohan Ramaraj, Long Qu, Richard Xiong, Surendran Kalathil, Rand Kato, Santhosh Tenkillaya, Jerry Carney, Rosann Redd, Sheshkumar Arkalgudvenkata, Kashif Shahzad, Richard Scott, Hui Cheng, Stephen Meadow, John McMichael, Shwu Lin Sheu, David Rosendale, Leonid KvecherStephen Ahern, Song Yang, Yonghong Zhang, Rick Jordan, Stella B. Somiari, Jeffrey Hooke, Craig D. Shriver, Richard I. Somiari, Micheal N. Liebman

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

25 Scopus citations

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. 2004

Original language	English
Pages (from-to)	933-941
Number of pages	9
Journal	Pharmacogenomics
Volume	5
Issue number	7
DOIs	https://doi.org/10.1517/14622416.5.7.933
State	Published - Oct 2004
Externally published	Yes

Keywords

Clinical information
Data warehouse
Federated
Genomics
Hybrid
Integrated
Proteomics

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Hu, H., Brzeski, H., Hutchins, J., Ramaraj, M., Qu, L., Xiong, R., Kalathil, S., Kato, R., Tenkillaya, S., Carney, J., Redd, R., Arkalgudvenkata, S., Shahzad, K., Scott, R., Cheng, H., Meadow, S., McMichael, J., Sheu, S. L., Rosendale, D., ... Liebman, M. N. (2004). Biomedical informatics: Development of a comprehensive data warehouse for clinical and genomic breast cancer research. Pharmacogenomics, 5(7), 933-941. https://doi.org/10.1517/14622416.5.7.933

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title = "Biomedical informatics: Development of a comprehensive data warehouse for clinical and genomic breast cancer research",

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. 2004",

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author = "Hai Hu and Henry Brzeski and Joe Hutchins and Mohan Ramaraj and Long Qu and Richard Xiong and Surendran Kalathil and Rand Kato and Santhosh Tenkillaya and Jerry Carney and Rosann Redd and Sheshkumar Arkalgudvenkata and Kashif Shahzad and Richard Scott and Hui Cheng and Stephen Meadow and John McMichael and Sheu, {Shwu Lin} and David Rosendale and Leonid Kvecher and Stephen Ahern and Song Yang and Yonghong Zhang and Rick Jordan and Somiari, {Stella B.} and Jeffrey Hooke and Shriver, {Craig D.} and Somiari, {Richard I.} and Liebman, {Micheal N.}",

year = "2004",

month = oct,

doi = "10.1517/14622416.5.7.933",

language = "English",

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Hu, H, Brzeski, H, Hutchins, J, Ramaraj, M, Qu, L, Xiong, R, Kalathil, S, Kato, R, Tenkillaya, S, Carney, J, Redd, R, Arkalgudvenkata, S, Shahzad, K, Scott, R, Cheng, H, Meadow, S, McMichael, J, Sheu, SL, Rosendale, D, Kvecher, L, Ahern, S, Yang, S, Zhang, Y, Jordan, R, Somiari, SB , Hooke, J , Shriver, CD, Somiari, RI & Liebman, MN 2004, 'Biomedical informatics: Development of a comprehensive data warehouse for clinical and genomic breast cancer research', Pharmacogenomics, vol. 5, no. 7, pp. 933-941. https://doi.org/10.1517/14622416.5.7.933

TY - JOUR

T1 - Biomedical informatics

T2 - Development of a comprehensive data warehouse for clinical and genomic breast cancer research

AU - Hu, Hai

AU - Brzeski, Henry

AU - Hutchins, Joe

AU - Ramaraj, Mohan

AU - Qu, Long

AU - Xiong, Richard

AU - Kalathil, Surendran

AU - Kato, Rand

AU - Tenkillaya, Santhosh

AU - Carney, Jerry

AU - Redd, Rosann

AU - Arkalgudvenkata, Sheshkumar

AU - Shahzad, Kashif

AU - Scott, Richard

AU - Cheng, Hui

AU - Meadow, Stephen

AU - McMichael, John

AU - Sheu, Shwu Lin

AU - Rosendale, David

AU - Kvecher, Leonid

AU - Ahern, Stephen

AU - Yang, Song

AU - Zhang, Yonghong

AU - Jordan, Rick

AU - Somiari, Stella B.

AU - Hooke, Jeffrey

AU - Shriver, Craig D.

AU - Somiari, Richard I.

AU - Liebman, Micheal N.

PY - 2004/10

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N2 - 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. 2004

AB - 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. 2004

KW - Clinical information

KW - Data warehouse

KW - Federated

KW - Genomics

KW - Hybrid

KW - Integrated

KW - Proteomics

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DO - 10.1517/14622416.5.7.933

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C2 - 15469411

AN - SCOPUS:6344278614

SN - 1462-2416

VL - 5

SP - 933

EP - 941

JO - Pharmacogenomics

JF - Pharmacogenomics

IS - 7

ER -

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

Abstract

Keywords

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